Harvest for Wallis et Futuna Species List Created 17 Oct 00:25

Stage: completed
Fetched: 17 Oct 00:25
Validated: 17 Oct 00:25
Deltas Created 17 Oct 00:25
Units Normalized: 17 Oct 00:26
Ancestry Built: 17 Oct 00:25
Nodes Matched: 17 Oct 00:26
Names Parsed: 17 Oct 00:25
New Models Stored: 17 Oct 00:25
Indexed: 17 Oct 00:26
Completed: 17 Oct 00:27
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-17 00:25:35 -0400 by logger.rb/56815
[START] [2019-10-17 00:25:35] logged process
[START] [2019-10-17 00:25:35] create_harvest_instance
[STOP] [2019-10-17 00:25:35] create_harvest_instance
[START] [2019-10-17 00:25:35] fetch_files
[STOP] [2019-10-17 00:25:35] fetch_files
[START] [2019-10-17 00:25:35] validate_each_file
[STOP] [2019-10-17 00:25:36] validate_each_file
[START] [2019-10-17 00:25:36] convert_to_csv
[CMD] [2019-10-17 00:25:36] /usr/bin/sort /app/public/converted_csv/wefsl_refs_17649.csv > /app/public/converted_csv/wefsl_refs_17649.csv_sorted
[CMD] [2019-10-17 00:25:36] /usr/bin/sort /app/public/converted_csv/wefsl_nodes_17650.csv > /app/public/converted_csv/wefsl_nodes_17650.csv_sorted
[CMD] [2019-10-17 00:25:36] /usr/bin/sort /app/public/converted_csv/wefsl_occurrences_17651.csv > /app/public/converted_csv/wefsl_occurrences_17651.csv_sorted
[CMD] [2019-10-17 00:25:36] /usr/bin/sort /app/public/converted_csv/wefsl_measurements_17652.csv > /app/public/converted_csv/wefsl_measurements_17652.csv_sorted
[STOP] [2019-10-17 00:25:36] convert_to_csv
[START] [2019-10-17 00:25:36] calculate_delta
[CMD] [2019-10-17 00:25:36] echo "0a" > /app/public/diff/wefsl_refs_17649.diff
[CMD] [2019-10-17 00:25:36] tail -n +1 /app/public/converted_csv/wefsl_refs_17649.csv >> /app/public/diff/wefsl_refs_17649.diff
[CMD] [2019-10-17 00:25:36] echo "." >> /app/public/diff/wefsl_refs_17649.diff
[CMD] [2019-10-17 00:25:36] echo "0a" > /app/public/diff/wefsl_nodes_17650.diff
[CMD] [2019-10-17 00:25:36] tail -n +1 /app/public/converted_csv/wefsl_nodes_17650.csv >> /app/public/diff/wefsl_nodes_17650.diff
[CMD] [2019-10-17 00:25:36] echo "." >> /app/public/diff/wefsl_nodes_17650.diff
[CMD] [2019-10-17 00:25:36] echo "0a" > /app/public/diff/wefsl_occurrences_17651.diff
[CMD] [2019-10-17 00:25:37] tail -n +1 /app/public/converted_csv/wefsl_occurrences_17651.csv >> /app/public/diff/wefsl_occurrences_17651.diff
[CMD] [2019-10-17 00:25:37] echo "." >> /app/public/diff/wefsl_occurrences_17651.diff
[CMD] [2019-10-17 00:25:37] echo "0a" > /app/public/diff/wefsl_measurements_17652.diff
[CMD] [2019-10-17 00:25:37] tail -n +1 /app/public/converted_csv/wefsl_measurements_17652.csv >> /app/public/diff/wefsl_measurements_17652.diff
[CMD] [2019-10-17 00:25:37] echo "." >> /app/public/diff/wefsl_measurements_17652.diff
[STOP] [2019-10-17 00:25:37] calculate_delta
[START] [2019-10-17 00:25:37] parse_diff_and_store
[INFO] [2019-10-17 00:25:37] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-17 00:25:37] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-17 00:25:37] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-17 00:25:37] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-17 00:25:38] Storing 2 References
[INFO] [2019-10-17 00:25:38] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-17 00:25:38] Average Time: 0.0
[INFO] [2019-10-17 00:25:38] Total Time: 1s
[INFO] [2019-10-17 00:25:38] Storing 226 ScientificNames
[INFO] [2019-10-17 00:25:38] Processing group of 226 in 1 groups of 1000
[INFO] [2019-10-17 00:25:38] Average Time: 0.25
[INFO] [2019-10-17 00:25:38] Total Time: 1s
[INFO] [2019-10-17 00:25:38] Storing 226 Nodes
[INFO] [2019-10-17 00:25:38] Processing group of 226 in 1 groups of 1000
[INFO] [2019-10-17 00:25:38] Average Time: 0.08
[INFO] [2019-10-17 00:25:38] Total Time: 1s
[INFO] [2019-10-17 00:25:38] Storing 71 Occurrences
[INFO] [2019-10-17 00:25:38] Processing group of 71 in 1 groups of 1000
[INFO] [2019-10-17 00:25:38] Average Time: 0.02
[INFO] [2019-10-17 00:25:38] Total Time: 1s
[INFO] [2019-10-17 00:25:38] Storing 142 TraitsReferences
[INFO] [2019-10-17 00:25:38] Processing group of 142 in 1 groups of 1000
[INFO] [2019-10-17 00:25:38] Average Time: 0.06
[INFO] [2019-10-17 00:25:38] Total Time: 1s
[INFO] [2019-10-17 00:25:38] Storing 142 Traits
[INFO] [2019-10-17 00:25:38] Processing group of 142 in 1 groups of 1000
[INFO] [2019-10-17 00:25:38] Average Time: 0.11
[INFO] [2019-10-17 00:25:38] Total Time: 1s
[INFO] [2019-10-17 00:25:38] Storing 142 MetaTraits
[INFO] [2019-10-17 00:25:38] Processing group of 142 in 1 groups of 1000
[INFO] [2019-10-17 00:25:39] Average Time: 0.04
[INFO] [2019-10-17 00:25:39] Total Time: 1s
[STOP] [2019-10-17 00:25:39] parse_diff_and_store
[START] [2019-10-17 00:25:39] resolve_keys
[INFO] [2019-10-17 00:25:42] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-17 00:25:42] traits to occurrences...
[INFO] [2019-10-17 00:25:43] traits to nodes (through occurrences)...
[INFO] [2019-10-17 00:25:43] Traits to sex term...
[INFO] [2019-10-17 00:25:43] Traits to lifestage term...
[INFO] [2019-10-17 00:25:43] MetaTraits to traits...
[INFO] [2019-10-17 00:25:43] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-17 00:25:43] Assocs to occurrences...
[INFO] [2019-10-17 00:25:43] Assocs to nodes...
[INFO] [2019-10-17 00:25:43] Assoc to sex term...
[INFO] [2019-10-17 00:25:43] Assoc to lifestage term...
[STOP] [2019-10-17 00:25:43] resolve_keys
[START] [2019-10-17 00:25:43] hold_for_later_1
[STOP] [2019-10-17 00:25:43] hold_for_later_1
[START] [2019-10-17 00:25:43] hold_for_later_2
[STOP] [2019-10-17 00:25:43] hold_for_later_2
[START] [2019-10-17 00:25:43] resolve_missing_parents
[STOP] [2019-10-17 00:25:43] resolve_missing_parents
[START] [2019-10-17 00:25:43] rebuild_nodes
[START] [2019-10-17 00:25:43] Flattener#flatten
[START] [2019-10-17 00:25:43] Flattener#study_resource
[START] [2019-10-17 00:25:43] Flattener#build_ancestry
[STOP] [2019-10-17 00:25:43] Flattener#build_ancestry
[INFO] [2019-10-17 00:25:43] 226 ancestry keys
[START] [2019-10-17 00:25:43] build_node_ancestors
[INFO] [2019-10-17 00:25:43] old ancestors deleted.
[STOP] [2019-10-17 00:25:43] build_node_ancestors
[START] [2019-10-17 00:25:43] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 00:25:43] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 00:25:43] Flattener#flatten
[STOP] [2019-10-17 00:25:43] rebuild_nodes
[START] [2019-10-17 00:25:43] resolve_missing_media_owners
[STOP] [2019-10-17 00:25:43] resolve_missing_media_owners
[START] [2019-10-17 00:25:43] sanitize_media_verbatims
[STOP] [2019-10-17 00:25:43] sanitize_media_verbatims
[START] [2019-10-17 00:25:43] queue_downloads
[STOP] [2019-10-17 00:25:43] queue_downloads
[START] [2019-10-17 00:25:43] parse_names
[WARN] [2019-10-17 00:25:43] I see 226 names which still need to be parsed.
[STOP] [2019-10-17 00:25:44] parse_names
[START] [2019-10-17 00:25:44] denormalize_canonical_names_to_nodes
[STOP] [2019-10-17 00:25:44] denormalize_canonical_names_to_nodes
[START] [2019-10-17 00:25:44] match_nodes
[START] [2019-10-17 00:25:44] map_all_nodes_to_pages
[STOP] [2019-10-17 00:26:03] map_all_nodes_to_pages
[INFO] [2019-10-17 00:26:03] Unmatched nodes (8 of 226): Dactylogyridea (#52681362); Pulmonata (#52681510); Neritopsina (#52681514); Veneroida (#52681497); Magnoliopsida (#52681383); Taccaceae (#52681464); Magnoliophyta (#52681419); Pteridophyta (#52681539)
[START] [2019-10-17 00:26:03] update_nodes
[STOP] [2019-10-17 00:26:03] update_nodes
[STOP] [2019-10-17 00:26:03] match_nodes
[START] [2019-10-17 00:26:03] reindex_search
[STOP] [2019-10-17 00:26:03] reindex_search
[START] [2019-10-17 00:26:03] normalize_units
[STOP] [2019-10-17 00:26:03] normalize_units
[START] [2019-10-17 00:26:03] calculate_statistics
[STOP] [2019-10-17 00:26:03] calculate_statistics
[START] [2019-10-17 00:26:03] complete_harvest_instance
[START] [2019-10-17 00:26:03] overall_tsv_creation
[INFO] [2019-10-17 00:26:03] Processing group of 226 in 1 batches of 10000
[INFO] [2019-10-17 00:26:46] 71 Traits (unfiltered)...
[INFO] [2019-10-17 00:26:59] 71 Traits (filtered)...
[INFO] [2019-10-17 00:26:59] 0 Associations (filtered)...
[INFO] [2019-10-17 00:27:35] 355 metadata added.
[INFO] [2019-10-17 00:27:35] 0 metadata added.
[INFO] [2019-10-17 00:27:35] Average Time: 71.27
[INFO] [2019-10-17 00:27:35] Total Time: 1m33s
[STOP] [2019-10-17 00:27:35] overall_tsv_creation
[INFO] [2019-10-17 00:27:35] Done. Check your files:
[INFO] [2019-10-17 00:27:35] (226 lines) /app/public/data/wefsl/publish_nodes.tsv
[INFO] [2019-10-17 00:27:35] (925 lines) /app/public/data/wefsl/publish_node_ancestors.tsv
[INFO] [2019-10-17 00:27:35] (226 lines) /app/public/data/wefsl/publish_scientific_names.tsv
[INFO] [2019-10-17 00:27:35] (72 lines) /app/public/data/wefsl/publish_traits.tsv
[INFO] [2019-10-17 00:27:35] (356 lines) /app/public/data/wefsl/publish_metadata.tsv
[STOP] [2019-10-17 00:27:36] complete_harvest_instance
[START] [2019-10-17 00:27:36] completed
[STOP] [2019-10-17 00:27:36] completed
[STOP] [2019-10-17 00:27:36] logged process, took 120.63
Latest Process

17 Oct 00:25 EXITED currently processing 0