Harvest for US Virgin Islands Species List Created 17 Oct 11:09

Stage: completed
Fetched: 17 Oct 11:09
Validated: 17 Oct 11:09
Deltas Created 17 Oct 11:09
Units Normalized: 17 Oct 11:10
Ancestry Built: 17 Oct 11:09
Nodes Matched: 17 Oct 11:10
Names Parsed: 17 Oct 11:09
New Models Stored: 17 Oct 11:09
Indexed: 17 Oct 11:10
Completed: 17 Oct 11:12
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-17 11:09:26 -0400 by logger.rb/56815
[START] [2019-10-17 11:09:26] logged process
[START] [2019-10-17 11:09:26] create_harvest_instance
[STOP] [2019-10-17 11:09:26] create_harvest_instance
[START] [2019-10-17 11:09:26] fetch_files
[STOP] [2019-10-17 11:09:26] fetch_files
[START] [2019-10-17 11:09:26] validate_each_file
[STOP] [2019-10-17 11:09:26] validate_each_file
[START] [2019-10-17 11:09:26] convert_to_csv
[CMD] [2019-10-17 11:09:26] /usr/bin/sort /app/public/converted_csv/uvisl_refs_17713.csv > /app/public/converted_csv/uvisl_refs_17713.csv_sorted
[CMD] [2019-10-17 11:09:27] /usr/bin/sort /app/public/converted_csv/uvisl_nodes_17714.csv > /app/public/converted_csv/uvisl_nodes_17714.csv_sorted
[CMD] [2019-10-17 11:09:27] /usr/bin/sort /app/public/converted_csv/uvisl_occurrences_17715.csv > /app/public/converted_csv/uvisl_occurrences_17715.csv_sorted
[CMD] [2019-10-17 11:09:27] /usr/bin/sort /app/public/converted_csv/uvisl_measurements_17716.csv > /app/public/converted_csv/uvisl_measurements_17716.csv_sorted
[STOP] [2019-10-17 11:09:27] convert_to_csv
[START] [2019-10-17 11:09:27] calculate_delta
[CMD] [2019-10-17 11:09:27] echo "0a" > /app/public/diff/uvisl_refs_17713.diff
[CMD] [2019-10-17 11:09:27] tail -n +1 /app/public/converted_csv/uvisl_refs_17713.csv >> /app/public/diff/uvisl_refs_17713.diff
[CMD] [2019-10-17 11:09:27] echo "." >> /app/public/diff/uvisl_refs_17713.diff
[CMD] [2019-10-17 11:09:27] echo "0a" > /app/public/diff/uvisl_nodes_17714.diff
[CMD] [2019-10-17 11:09:27] tail -n +1 /app/public/converted_csv/uvisl_nodes_17714.csv >> /app/public/diff/uvisl_nodes_17714.diff
[CMD] [2019-10-17 11:09:27] echo "." >> /app/public/diff/uvisl_nodes_17714.diff
[CMD] [2019-10-17 11:09:27] echo "0a" > /app/public/diff/uvisl_occurrences_17715.diff
[CMD] [2019-10-17 11:09:27] tail -n +1 /app/public/converted_csv/uvisl_occurrences_17715.csv >> /app/public/diff/uvisl_occurrences_17715.diff
[CMD] [2019-10-17 11:09:28] echo "." >> /app/public/diff/uvisl_occurrences_17715.diff
[CMD] [2019-10-17 11:09:28] echo "0a" > /app/public/diff/uvisl_measurements_17716.diff
[CMD] [2019-10-17 11:09:28] tail -n +1 /app/public/converted_csv/uvisl_measurements_17716.csv >> /app/public/diff/uvisl_measurements_17716.diff
[CMD] [2019-10-17 11:09:28] echo "." >> /app/public/diff/uvisl_measurements_17716.diff
[STOP] [2019-10-17 11:09:28] calculate_delta
[START] [2019-10-17 11:09:28] parse_diff_and_store
[INFO] [2019-10-17 11:09:28] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-17 11:09:28] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-17 11:09:29] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-17 11:09:29] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-17 11:09:33] Storing 2 References
[INFO] [2019-10-17 11:09:33] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-17 11:09:33] Average Time: 0.0
[INFO] [2019-10-17 11:09:33] Total Time: 1s
[INFO] [2019-10-17 11:09:33] Storing 1802 ScientificNames
[INFO] [2019-10-17 11:09:33] Processing group of 1802 in 2 groups of 1000
[INFO] [2019-10-17 11:09:34] Average Time: 0.425
[INFO] [2019-10-17 11:09:34] Total Time: 1s
[INFO] [2019-10-17 11:09:34] Storing 1802 Nodes
[INFO] [2019-10-17 11:09:34] Processing group of 1802 in 2 groups of 1000
[INFO] [2019-10-17 11:09:35] Average Time: 0.27
[INFO] [2019-10-17 11:09:35] Total Time: 1s
[INFO] [2019-10-17 11:09:35] Storing 482 Occurrences
[INFO] [2019-10-17 11:09:35] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-17 11:09:35] Average Time: 0.06
[INFO] [2019-10-17 11:09:35] Total Time: 1s
[INFO] [2019-10-17 11:09:35] Storing 1570 TraitsReferences
[INFO] [2019-10-17 11:09:35] Processing group of 1570 in 2 groups of 1000
[INFO] [2019-10-17 11:09:35] Average Time: 0.08
[INFO] [2019-10-17 11:09:35] Total Time: 1s
[INFO] [2019-10-17 11:09:35] Storing 1569 Traits
[INFO] [2019-10-17 11:09:35] Processing group of 1569 in 2 groups of 1000
[INFO] [2019-10-17 11:09:36] Average Time: 0.27
[INFO] [2019-10-17 11:09:36] Total Time: 1s
[INFO] [2019-10-17 11:09:36] Storing 1570 MetaTraits
[INFO] [2019-10-17 11:09:36] Processing group of 1570 in 2 groups of 1000
[INFO] [2019-10-17 11:09:36] Average Time: 0.105
[INFO] [2019-10-17 11:09:36] Total Time: 1s
[STOP] [2019-10-17 11:09:36] parse_diff_and_store
[START] [2019-10-17 11:09:36] resolve_keys
[INFO] [2019-10-17 11:09:45] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-17 11:09:46] traits to occurrences...
[INFO] [2019-10-17 11:09:47] traits to nodes (through occurrences)...
[INFO] [2019-10-17 11:09:47] Traits to sex term...
[INFO] [2019-10-17 11:09:47] Traits to lifestage term...
[INFO] [2019-10-17 11:09:48] MetaTraits to traits...
[INFO] [2019-10-17 11:09:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-17 11:09:48] Assocs to occurrences...
[INFO] [2019-10-17 11:09:48] Assocs to nodes...
[INFO] [2019-10-17 11:09:48] Assoc to sex term...
[INFO] [2019-10-17 11:09:48] Assoc to lifestage term...
[STOP] [2019-10-17 11:09:48] resolve_keys
[START] [2019-10-17 11:09:48] hold_for_later_1
[STOP] [2019-10-17 11:09:48] hold_for_later_1
[START] [2019-10-17 11:09:48] hold_for_later_2
[STOP] [2019-10-17 11:09:48] hold_for_later_2
[START] [2019-10-17 11:09:48] resolve_missing_parents
[STOP] [2019-10-17 11:09:52] resolve_missing_parents
[START] [2019-10-17 11:09:52] rebuild_nodes
[START] [2019-10-17 11:09:52] Flattener#flatten
[START] [2019-10-17 11:09:52] Flattener#study_resource
[START] [2019-10-17 11:09:52] Flattener#build_ancestry
[STOP] [2019-10-17 11:09:52] Flattener#build_ancestry
[INFO] [2019-10-17 11:09:52] 1802 ancestry keys
[START] [2019-10-17 11:09:52] build_node_ancestors
[INFO] [2019-10-17 11:09:52] old ancestors deleted.
[STOP] [2019-10-17 11:09:52] build_node_ancestors
[START] [2019-10-17 11:09:52] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:09:53] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:09:53] Flattener#flatten
[STOP] [2019-10-17 11:09:53] rebuild_nodes
[START] [2019-10-17 11:09:53] resolve_missing_media_owners
[STOP] [2019-10-17 11:09:53] resolve_missing_media_owners
[START] [2019-10-17 11:09:53] sanitize_media_verbatims
[STOP] [2019-10-17 11:09:53] sanitize_media_verbatims
[START] [2019-10-17 11:09:53] queue_downloads
[STOP] [2019-10-17 11:09:53] queue_downloads
[START] [2019-10-17 11:09:53] parse_names
[WARN] [2019-10-17 11:09:53] I see 1802 names which still need to be parsed.
[STOP] [2019-10-17 11:09:55] parse_names
[START] [2019-10-17 11:09:55] denormalize_canonical_names_to_nodes
[STOP] [2019-10-17 11:09:55] denormalize_canonical_names_to_nodes
[START] [2019-10-17 11:09:55] match_nodes
[START] [2019-10-17 11:09:55] map_all_nodes_to_pages
[STOP] [2019-10-17 11:10:55] map_all_nodes_to_pages
[INFO] [2019-10-17 11:10:55] 68 Unmatched nodes (of 1802)! That's too many to output. First 10: Coerebidae (#52713149); Dendroica (#52713408); Dendroica petechia (#52713407); Oreothlypis celata (#52714632); Anas discors (#52713204); Anas clypeata (#52714087); Anas americana (#52714626); Limnodromus (#52713309); Thalaseus (#52713248); Thalaseus maximus (#52713247)
[START] [2019-10-17 11:10:55] update_nodes
[STOP] [2019-10-17 11:10:55] update_nodes
[STOP] [2019-10-17 11:10:55] match_nodes
[START] [2019-10-17 11:10:55] reindex_search
[STOP] [2019-10-17 11:10:57] reindex_search
[START] [2019-10-17 11:10:57] normalize_units
[STOP] [2019-10-17 11:10:57] normalize_units
[START] [2019-10-17 11:10:58] calculate_statistics
[STOP] [2019-10-17 11:10:58] calculate_statistics
[START] [2019-10-17 11:10:58] complete_harvest_instance
[START] [2019-10-17 11:10:58] overall_tsv_creation
[INFO] [2019-10-17 11:10:58] Processing group of 1802 in 1 batches of 10000
[INFO] [2019-10-17 11:11:48] 482 Traits (unfiltered)...
[INFO] [2019-10-17 11:12:01] 482 Traits (filtered)...
[INFO] [2019-10-17 11:12:01] 0 Associations (filtered)...
[INFO] [2019-10-17 11:12:38] 2410 metadata added.
[INFO] [2019-10-17 11:12:38] 0 metadata added.
[INFO] [2019-10-17 11:12:38] Average Time: 78.13
[INFO] [2019-10-17 11:12:38] Total Time: 1m41s
[STOP] [2019-10-17 11:12:38] overall_tsv_creation
[INFO] [2019-10-17 11:12:38] Done. Check your files:
[INFO] [2019-10-17 11:12:39] (1802 lines) /app/public/data/uvisl/publish_nodes.tsv
[INFO] [2019-10-17 11:12:39] (3686 lines) /app/public/data/uvisl/publish_node_ancestors.tsv
[INFO] [2019-10-17 11:12:39] (1802 lines) /app/public/data/uvisl/publish_scientific_names.tsv
[INFO] [2019-10-17 11:12:39] (483 lines) /app/public/data/uvisl/publish_traits.tsv
[INFO] [2019-10-17 11:12:39] (2411 lines) /app/public/data/uvisl/publish_metadata.tsv
[STOP] [2019-10-17 11:12:39] complete_harvest_instance
[START] [2019-10-17 11:12:39] completed
[STOP] [2019-10-17 11:12:39] completed
[STOP] [2019-10-17 11:12:39] logged process, took 193.31
Latest Process

17 Oct 11:09 EXITED currently processing 0