Harvest for Miller and Pawson 1990 Created 30 Jul 14:51

Harvesting Log

# Logfile created on 2020-07-30 14:45:26 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 14:45:26] logged process
[START] [2020-07-30 14:45:26] Creating resource from OpenData
[START] [2020-07-30 14:45:27] logged process
[START] [2020-07-30 14:45:27] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:45:27] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:45:27] Creating resource from OpenData
[INFO] [2020-07-30 14:45:29] ## HARVEST: type = -harvest
[START] [2020-07-30 14:45:32] logged process
[START] [2020-07-30 14:45:32] create_harvest_instance
[STOP] [2020-07-30 14:45:33] create_harvest_instance
[START] [2020-07-30 14:45:33] fetch_files
[STOP] [2020-07-30 14:45:33] fetch_files
[START] [2020-07-30 14:45:33] validate_each_file
[STOP] [2020-07-30 14:45:33] validate_each_file
[START] [2020-07-30 14:45:33] convert_to_csv
[CMD] [2020-07-30 14:45:33] /usr/bin/sort /app/public/converted_csv/miller_pawson_mi_refs_22300.csv > /app/public/converted_csv/miller_pawson_mi_refs_22300.csv_sorted
[CMD] [2020-07-30 14:45:33] /usr/bin/sort /app/public/converted_csv/miller_pawson_mi_nodes_22301.csv > /app/public/converted_csv/miller_pawson_mi_nodes_22301.csv_sorted
[CMD] [2020-07-30 14:45:33] /usr/bin/sort /app/public/converted_csv/miller_pawson_mi_occurrences_22302.csv > /app/public/converted_csv/miller_pawson_mi_occurrences_22302.csv_sorted
[CMD] [2020-07-30 14:45:33] /usr/bin/sort /app/public/converted_csv/miller_pawson_mi_measurements_22303.csv > /app/public/converted_csv/miller_pawson_mi_measurements_22303.csv_sorted
[STOP] [2020-07-30 14:45:33] convert_to_csv
[START] [2020-07-30 14:45:33] calculate_delta
[CMD] [2020-07-30 14:45:33] echo "0a" > /app/public/diff/miller_pawson_mi_refs_22300.diff
[CMD] [2020-07-30 14:45:33] tail -n +1 /app/public/converted_csv/miller_pawson_mi_refs_22300.csv >> /app/public/diff/miller_pawson_mi_refs_22300.diff
[CMD] [2020-07-30 14:45:33] echo "." >> /app/public/diff/miller_pawson_mi_refs_22300.diff
[CMD] [2020-07-30 14:45:33] echo "0a" > /app/public/diff/miller_pawson_mi_nodes_22301.diff
[CMD] [2020-07-30 14:45:33] tail -n +1 /app/public/converted_csv/miller_pawson_mi_nodes_22301.csv >> /app/public/diff/miller_pawson_mi_nodes_22301.diff
[CMD] [2020-07-30 14:45:33] echo "." >> /app/public/diff/miller_pawson_mi_nodes_22301.diff
[CMD] [2020-07-30 14:45:33] echo "0a" > /app/public/diff/miller_pawson_mi_occurrences_22302.diff
[CMD] [2020-07-30 14:45:33] tail -n +1 /app/public/converted_csv/miller_pawson_mi_occurrences_22302.csv >> /app/public/diff/miller_pawson_mi_occurrences_22302.diff
[CMD] [2020-07-30 14:45:33] echo "." >> /app/public/diff/miller_pawson_mi_occurrences_22302.diff
[CMD] [2020-07-30 14:45:33] echo "0a" > /app/public/diff/miller_pawson_mi_measurements_22303.diff
[CMD] [2020-07-30 14:45:33] tail -n +1 /app/public/converted_csv/miller_pawson_mi_measurements_22303.csv >> /app/public/diff/miller_pawson_mi_measurements_22303.diff
[CMD] [2020-07-30 14:45:33] echo "." >> /app/public/diff/miller_pawson_mi_measurements_22303.diff
[STOP] [2020-07-30 14:45:33] calculate_delta
[START] [2020-07-30 14:45:33] parse_diff_and_store
[INFO] [2020-07-30 14:45:33] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 14:45:33] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 14:45:33] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 14:45:33] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 14:45:34] Storing 37 References
[INFO] [2020-07-30 14:45:34] Processing group of 37 in 1 groups of 1000
[INFO] [2020-07-30 14:45:34] Average Time: 0.01
[INFO] [2020-07-30 14:45:34] Total Time: 1s
[INFO] [2020-07-30 14:45:34] Storing 25 ScientificNames
[INFO] [2020-07-30 14:45:34] Processing group of 25 in 1 groups of 1000
[INFO] [2020-07-30 14:45:34] Average Time: 0.01
[INFO] [2020-07-30 14:45:34] Total Time: 1s
[INFO] [2020-07-30 14:45:34] Storing 25 Nodes
[INFO] [2020-07-30 14:45:34] Processing group of 25 in 1 groups of 1000
[INFO] [2020-07-30 14:45:34] Average Time: 0.01
[INFO] [2020-07-30 14:45:34] Total Time: 1s
[INFO] [2020-07-30 14:45:34] Storing 25 Occurrences
[INFO] [2020-07-30 14:45:34] Processing group of 25 in 1 groups of 1000
[INFO] [2020-07-30 14:45:34] Average Time: 0.0
[INFO] [2020-07-30 14:45:34] Total Time: 1s
[INFO] [2020-07-30 14:45:34] Storing 3 OccurrenceMetadata
[INFO] [2020-07-30 14:45:34] Processing group of 3 in 1 groups of 1000
[INFO] [2020-07-30 14:45:34] Average Time: 0.02
[INFO] [2020-07-30 14:45:34] Total Time: 1s
[INFO] [2020-07-30 14:45:34] Storing 25 Traits
[INFO] [2020-07-30 14:45:34] Processing group of 25 in 1 groups of 1000
[INFO] [2020-07-30 14:45:34] Average Time: 0.01
[INFO] [2020-07-30 14:45:34] Total Time: 1s
[INFO] [2020-07-30 14:45:34] Storing 58 MetaTraits
[INFO] [2020-07-30 14:45:34] Processing group of 58 in 1 groups of 1000
[INFO] [2020-07-30 14:45:34] Average Time: 0.01
[INFO] [2020-07-30 14:45:34] Total Time: 1s
[INFO] [2020-07-30 14:45:34] Storing 50 TraitsReferences
[INFO] [2020-07-30 14:45:34] Processing group of 50 in 1 groups of 1000
[INFO] [2020-07-30 14:45:34] Average Time: 0.01
[INFO] [2020-07-30 14:45:34] Total Time: 1s
[STOP] [2020-07-30 14:45:34] parse_diff_and_store
[START] [2020-07-30 14:45:34] resolve_keys
[INFO] [2020-07-30 14:45:41] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 14:45:41] traits to occurrences...
[INFO] [2020-07-30 14:45:41] traits to nodes (through occurrences)...
[INFO] [2020-07-30 14:45:41] Traits to sex term...
[INFO] [2020-07-30 14:45:41] Traits to lifestage term...
[INFO] [2020-07-30 14:45:41] MetaTraits to traits...
[INFO] [2020-07-30 14:45:41] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 14:45:41] Assocs to occurrences...
[INFO] [2020-07-30 14:45:41] Assocs to nodes...
[INFO] [2020-07-30 14:45:41] Assoc to sex term...
[INFO] [2020-07-30 14:45:41] Assoc to lifestage term...
[STOP] [2020-07-30 14:45:41] resolve_keys
[START] [2020-07-30 14:45:41] hold_for_later_1
[STOP] [2020-07-30 14:45:41] hold_for_later_1
[START] [2020-07-30 14:45:41] hold_for_later_2
[STOP] [2020-07-30 14:45:41] hold_for_later_2
[START] [2020-07-30 14:45:41] resolve_missing_parents
[STOP] [2020-07-30 14:45:41] resolve_missing_parents
[START] [2020-07-30 14:45:41] rebuild_nodes
[START] [2020-07-30 14:45:41] Flattener#flatten
[START] [2020-07-30 14:45:41] Flattener#study_resource
[START] [2020-07-30 14:45:41] Flattener#build_ancestry
[STOP] [2020-07-30 14:45:41] Flattener#build_ancestry
[INFO] [2020-07-30 14:45:41] 25 ancestry keys
[START] [2020-07-30 14:45:41] build_node_ancestors
[INFO] [2020-07-30 14:45:41] old ancestors deleted.
[STOP] [2020-07-30 14:45:41] build_node_ancestors
[WARN] [2020-07-30 14:45:41] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 14:45:41] Flattener#flatten
[STOP] [2020-07-30 14:45:41] rebuild_nodes
[START] [2020-07-30 14:45:41] resolve_missing_media_owners
[STOP] [2020-07-30 14:45:41] resolve_missing_media_owners
[START] [2020-07-30 14:45:41] sanitize_media_verbatims
[STOP] [2020-07-30 14:45:41] sanitize_media_verbatims
[START] [2020-07-30 14:45:41] queue_downloads
[STOP] [2020-07-30 14:45:41] queue_downloads
[START] [2020-07-30 14:45:41] parse_names
[WARN] [2020-07-30 14:45:41] I see 25 names which still need to be parsed.
[WARN] [2020-07-30 14:45:42] I see 2 names which still need to be parsed.
[STOP] [2020-07-30 14:45:43] parse_names
[START] [2020-07-30 14:45:43] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 14:45:43] denormalize_canonical_names_to_nodes
[START] [2020-07-30 14:45:43] match_nodes
[START] [2020-07-30 14:45:43] map_all_nodes_to_pages
[STOP] [2020-07-30 14:45:43] map_all_nodes_to_pages
[INFO] [2020-07-30 14:45:43] ZERO unmatched nodes (of 25)! Nicely done.
[START] [2020-07-30 14:45:43] update_nodes
[STOP] [2020-07-30 14:45:43] update_nodes
[STOP] [2020-07-30 14:45:43] match_nodes
[START] [2020-07-30 14:45:43] reindex_search
[STOP] [2020-07-30 14:45:43] reindex_search
[START] [2020-07-30 14:45:43] normalize_units
[STOP] [2020-07-30 14:45:43] normalize_units
[START] [2020-07-30 14:45:43] calculate_statistics
[2020-07-30 14:45:43] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 14:45:43] calculate_statistics
[START] [2020-07-30 14:45:43] complete_harvest_instance
[START] [2020-07-30 14:45:43] overall_tsv_creation
[INFO] [2020-07-30 14:45:43] Processing group of 25 in 1 batches of 10000
[INFO] [2020-07-30 14:46:32] 25 Traits (unfiltered)...
[INFO] [2020-07-30 14:47:09] 25 Traits (filtered)...
[INFO] [2020-07-30 14:47:09] 0 Associations (filtered)...
[INFO] [2020-07-30 14:47:09] 110 metadata added.
[INFO] [2020-07-30 14:47:09] 0 metadata added.
[INFO] [2020-07-30 14:47:09] Average Time: 58.24
[INFO] [2020-07-30 14:47:09] Total Time: 1m26s
[STOP] [2020-07-30 14:47:09] overall_tsv_creation
[INFO] [2020-07-30 14:47:09] Done. Check your files:
[INFO] [2020-07-30 14:47:09] (23 lines) /app/public/data/miller_pawson_mi/publish_nodes.tsv
[INFO] [2020-07-30 14:47:09] (25 lines) /app/public/data/miller_pawson_mi/publish_scientific_names.tsv
[INFO] [2020-07-30 14:47:09] (26 lines) /app/public/data/miller_pawson_mi/publish_traits.tsv
[INFO] [2020-07-30 14:47:09] (53 lines) /app/public/data/miller_pawson_mi/publish_metadata.tsv
[STOP] [2020-07-30 14:47:09] complete_harvest_instance
[START] [2020-07-30 14:47:09] completed
[STOP] [2020-07-30 14:47:09] completed
[STOP] [2020-07-30 14:47:09] logged process, took 96.87
[INFO] [2020-07-30 14:51:33] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-07-30 14:51:37] ## remove_type: ScientificName
[INFO] [2020-07-30 14:51:37] ++ Calling delete_all on 25 instances...
[INFO] [2020-07-30 14:51:37] [14:51:37.681] Removed 25 Scientificnames
[INFO] [2020-07-30 14:51:37] ## remove_type: Vernacular
[INFO] [2020-07-30 14:51:37] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:51:37] [14:51:37.684] Removed 0 Vernaculars
[INFO] [2020-07-30 14:51:37] ## remove_type: Article
[INFO] [2020-07-30 14:51:37] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:51:37] [14:51:37.687] Removed 0 Articles
[INFO] [2020-07-30 14:51:37] ## remove_type: Medium
[INFO] [2020-07-30 14:51:37] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:51:37] [14:51:37.690] Removed 0 Media
[INFO] [2020-07-30 14:51:37] ## remove_type: Trait
[INFO] [2020-07-30 14:51:37] ++ Calling delete_all on 25 instances...
[INFO] [2020-07-30 14:51:37] [14:51:37.694] Removed 25 Traits
[INFO] [2020-07-30 14:51:37] ## remove_type: MetaTrait
[INFO] [2020-07-30 14:51:37] ++ Calling delete_all on 58 instances...
[INFO] [2020-07-30 14:51:37] [14:51:37.698] Removed 58 Metatraits
[INFO] [2020-07-30 14:51:37] ## remove_type: OccurrenceMetadatum
[INFO] [2020-07-30 14:51:37] ++ Calling delete_all on 3 instances...
[INFO] [2020-07-30 14:51:37] [14:51:37.701] Removed 3 Occurrencemetadata
[INFO] [2020-07-30 14:51:37] ## remove_type: Assoc
[INFO] [2020-07-30 14:51:37] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:51:37] [14:51:37.703] Removed 0 Assocs
[INFO] [2020-07-30 14:51:37] ## remove_type: MetaAssoc
[INFO] [2020-07-30 14:51:37] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:51:37] [14:51:37.707] Removed 0 Metaassocs
[INFO] [2020-07-30 14:51:37] ## remove_type: Identifier
[INFO] [2020-07-30 14:51:37] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:51:37] [14:51:37.709] Removed 0 Identifiers
[INFO] [2020-07-30 14:51:37] ## remove_type: Reference
[INFO] [2020-07-30 14:51:37] ++ Calling delete_all on 37 instances...
[INFO] [2020-07-30 14:51:37] [14:51:37.713] Removed 37 References
[INFO] [2020-07-30 14:51:37] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:37] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:37] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:37] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:37] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:37] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:37] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:37] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:37] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:37] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:37] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:38] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:38] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:38] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:38] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:38] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:38] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:38] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:38] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:38] Starting batch with ID 80634412...
[INFO] [2020-07-30 14:51:38] Starting batch with ID 80634417...
[INFO] [2020-07-30 14:51:38] Starting batch with ID 80634414...
[INFO] [2020-07-30 14:51:38] ## remove_type: Node
[INFO] [2020-07-30 14:51:38] ++ Calling delete_all on 25 instances...
[INFO] [2020-07-30 14:51:38] [14:51:38.528] Removed 25 Nodes
[START] [2020-07-30 14:51:38] logged process
[START] [2020-07-30 14:51:38] Creating resource from OpenData
[START] [2020-07-30 14:51:38] logged process
[START] [2020-07-30 14:51:38] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:51:39] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:51:39] Creating resource from OpenData
[START] [2020-07-30 14:51:39] logged process
[START] [2020-07-30 14:51:39] create_harvest_instance
[STOP] [2020-07-30 14:51:40] create_harvest_instance
[START] [2020-07-30 14:51:40] fetch_files
[STOP] [2020-07-30 14:51:40] fetch_files
[START] [2020-07-30 14:51:40] validate_each_file
[STOP] [2020-07-30 14:51:40] validate_each_file
[START] [2020-07-30 14:51:40] convert_to_csv
[CMD] [2020-07-30 14:51:40] /usr/bin/sort /app/public/converted_csv/miller_pawson_mi_refs_22324.csv > /app/public/converted_csv/miller_pawson_mi_refs_22324.csv_sorted
[CMD] [2020-07-30 14:51:40] /usr/bin/sort /app/public/converted_csv/miller_pawson_mi_nodes_22325.csv > /app/public/converted_csv/miller_pawson_mi_nodes_22325.csv_sorted
[CMD] [2020-07-30 14:51:40] /usr/bin/sort /app/public/converted_csv/miller_pawson_mi_occurrences_22326.csv > /app/public/converted_csv/miller_pawson_mi_occurrences_22326.csv_sorted
[CMD] [2020-07-30 14:51:40] /usr/bin/sort /app/public/converted_csv/miller_pawson_mi_measurements_22327.csv > /app/public/converted_csv/miller_pawson_mi_measurements_22327.csv_sorted
[STOP] [2020-07-30 14:51:40] convert_to_csv
[START] [2020-07-30 14:51:40] calculate_delta
[CMD] [2020-07-30 14:51:40] echo "0a" > /app/public/diff/miller_pawson_mi_refs_22324.diff
[CMD] [2020-07-30 14:51:40] tail -n +1 /app/public/converted_csv/miller_pawson_mi_refs_22324.csv >> /app/public/diff/miller_pawson_mi_refs_22324.diff
[CMD] [2020-07-30 14:51:40] echo "." >> /app/public/diff/miller_pawson_mi_refs_22324.diff
[CMD] [2020-07-30 14:51:40] echo "0a" > /app/public/diff/miller_pawson_mi_nodes_22325.diff
[CMD] [2020-07-30 14:51:40] tail -n +1 /app/public/converted_csv/miller_pawson_mi_nodes_22325.csv >> /app/public/diff/miller_pawson_mi_nodes_22325.diff
[CMD] [2020-07-30 14:51:40] echo "." >> /app/public/diff/miller_pawson_mi_nodes_22325.diff
[CMD] [2020-07-30 14:51:40] echo "0a" > /app/public/diff/miller_pawson_mi_occurrences_22326.diff
[CMD] [2020-07-30 14:51:40] tail -n +1 /app/public/converted_csv/miller_pawson_mi_occurrences_22326.csv >> /app/public/diff/miller_pawson_mi_occurrences_22326.diff
[CMD] [2020-07-30 14:51:40] echo "." >> /app/public/diff/miller_pawson_mi_occurrences_22326.diff
[CMD] [2020-07-30 14:51:40] echo "0a" > /app/public/diff/miller_pawson_mi_measurements_22327.diff
[CMD] [2020-07-30 14:51:40] tail -n +1 /app/public/converted_csv/miller_pawson_mi_measurements_22327.csv >> /app/public/diff/miller_pawson_mi_measurements_22327.diff
[CMD] [2020-07-30 14:51:40] echo "." >> /app/public/diff/miller_pawson_mi_measurements_22327.diff
[STOP] [2020-07-30 14:51:40] calculate_delta
[START] [2020-07-30 14:51:40] parse_diff_and_store
[INFO] [2020-07-30 14:51:40] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 14:51:40] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 14:51:40] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 14:51:40] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 14:51:41] Storing 37 References
[INFO] [2020-07-30 14:51:41] Processing group of 37 in 1 groups of 1000
[INFO] [2020-07-30 14:51:41] Average Time: 0.02
[INFO] [2020-07-30 14:51:41] Total Time: 1s
[INFO] [2020-07-30 14:51:41] Storing 25 ScientificNames
[INFO] [2020-07-30 14:51:41] Processing group of 25 in 1 groups of 1000
[INFO] [2020-07-30 14:51:41] Average Time: 0.01
[INFO] [2020-07-30 14:51:41] Total Time: 1s
[INFO] [2020-07-30 14:51:41] Storing 25 Nodes
[INFO] [2020-07-30 14:51:41] Processing group of 25 in 1 groups of 1000
[INFO] [2020-07-30 14:51:41] Average Time: 0.01
[INFO] [2020-07-30 14:51:41] Total Time: 1s
[INFO] [2020-07-30 14:51:41] Storing 25 Occurrences
[INFO] [2020-07-30 14:51:41] Processing group of 25 in 1 groups of 1000
[INFO] [2020-07-30 14:51:41] Average Time: 0.0
[INFO] [2020-07-30 14:51:41] Total Time: 1s
[INFO] [2020-07-30 14:51:41] Storing 3 OccurrenceMetadata
[INFO] [2020-07-30 14:51:41] Processing group of 3 in 1 groups of 1000
[INFO] [2020-07-30 14:51:41] Average Time: 0.0
[INFO] [2020-07-30 14:51:41] Total Time: 1s
[INFO] [2020-07-30 14:51:41] Storing 25 Traits
[INFO] [2020-07-30 14:51:41] Processing group of 25 in 1 groups of 1000
[INFO] [2020-07-30 14:51:41] Average Time: 0.01
[INFO] [2020-07-30 14:51:41] Total Time: 1s
[INFO] [2020-07-30 14:51:41] Storing 58 MetaTraits
[INFO] [2020-07-30 14:51:41] Processing group of 58 in 1 groups of 1000
[INFO] [2020-07-30 14:51:41] Average Time: 0.01
[INFO] [2020-07-30 14:51:41] Total Time: 1s
[INFO] [2020-07-30 14:51:41] Storing 50 TraitsReferences
[INFO] [2020-07-30 14:51:41] Processing group of 50 in 1 groups of 1000
[INFO] [2020-07-30 14:51:41] Average Time: 0.03
[INFO] [2020-07-30 14:51:41] Total Time: 1s
[STOP] [2020-07-30 14:51:41] parse_diff_and_store
[START] [2020-07-30 14:51:41] resolve_keys
[INFO] [2020-07-30 14:51:47] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 14:51:47] traits to occurrences...
[INFO] [2020-07-30 14:51:47] traits to nodes (through occurrences)...
[INFO] [2020-07-30 14:51:47] Traits to sex term...
[INFO] [2020-07-30 14:51:47] Traits to lifestage term...
[INFO] [2020-07-30 14:51:47] MetaTraits to traits...
[INFO] [2020-07-30 14:51:47] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 14:51:47] Assocs to occurrences...
[INFO] [2020-07-30 14:51:47] Assocs to nodes...
[INFO] [2020-07-30 14:51:47] Assoc to sex term...
[INFO] [2020-07-30 14:51:47] Assoc to lifestage term...
[STOP] [2020-07-30 14:51:47] resolve_keys
[START] [2020-07-30 14:51:47] hold_for_later_1
[STOP] [2020-07-30 14:51:47] hold_for_later_1
[START] [2020-07-30 14:51:47] hold_for_later_2
[STOP] [2020-07-30 14:51:47] hold_for_later_2
[START] [2020-07-30 14:51:47] resolve_missing_parents
[STOP] [2020-07-30 14:51:47] resolve_missing_parents
[START] [2020-07-30 14:51:47] rebuild_nodes
[START] [2020-07-30 14:51:47] Flattener#flatten
[START] [2020-07-30 14:51:47] Flattener#study_resource
[START] [2020-07-30 14:51:47] Flattener#build_ancestry
[STOP] [2020-07-30 14:51:47] Flattener#build_ancestry
[INFO] [2020-07-30 14:51:47] 25 ancestry keys
[START] [2020-07-30 14:51:47] build_node_ancestors
[INFO] [2020-07-30 14:51:47] old ancestors deleted.
[STOP] [2020-07-30 14:51:47] build_node_ancestors
[WARN] [2020-07-30 14:51:48] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 14:51:48] Flattener#flatten
[STOP] [2020-07-30 14:51:48] rebuild_nodes
[START] [2020-07-30 14:51:48] resolve_missing_media_owners
[STOP] [2020-07-30 14:51:48] resolve_missing_media_owners
[START] [2020-07-30 14:51:48] sanitize_media_verbatims
[STOP] [2020-07-30 14:51:48] sanitize_media_verbatims
[START] [2020-07-30 14:51:48] queue_downloads
[STOP] [2020-07-30 14:51:48] queue_downloads
[START] [2020-07-30 14:51:48] parse_names
[WARN] [2020-07-30 14:51:48] I see 25 names which still need to be parsed.
[WARN] [2020-07-30 14:51:49] I see 2 names which still need to be parsed.
[STOP] [2020-07-30 14:51:50] parse_names
[START] [2020-07-30 14:51:50] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 14:51:50] denormalize_canonical_names_to_nodes
[START] [2020-07-30 14:51:50] match_nodes
[START] [2020-07-30 14:51:50] map_all_nodes_to_pages
[STOP] [2020-07-30 14:51:50] map_all_nodes_to_pages
[INFO] [2020-07-30 14:51:50] ZERO unmatched nodes (of 25)! Nicely done.
[START] [2020-07-30 14:51:50] update_nodes
[STOP] [2020-07-30 14:51:50] update_nodes
[STOP] [2020-07-30 14:51:50] match_nodes
[START] [2020-07-30 14:51:50] reindex_search
[STOP] [2020-07-30 14:51:50] reindex_search
[START] [2020-07-30 14:51:50] normalize_units
[STOP] [2020-07-30 14:51:50] normalize_units
[START] [2020-07-30 14:51:50] calculate_statistics
[2020-07-30 14:51:50] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 14:51:50] calculate_statistics
[START] [2020-07-30 14:51:50] complete_harvest_instance
[START] [2020-07-30 14:51:50] overall_tsv_creation
[INFO] [2020-07-30 14:51:50] Processing group of 25 in 1 batches of 10000
[INFO] [2020-07-30 14:52:40] 25 Traits (unfiltered)...
[INFO] [2020-07-30 14:53:16] 25 Traits (filtered)...
[INFO] [2020-07-30 14:53:16] 0 Associations (filtered)...
[INFO] [2020-07-30 14:53:16] 110 metadata added.
[INFO] [2020-07-30 14:53:16] 0 metadata added.
[INFO] [2020-07-30 14:53:16] Average Time: 58.53
[INFO] [2020-07-30 14:53:16] Total Time: 1m26s
[STOP] [2020-07-30 14:53:16] overall_tsv_creation
[INFO] [2020-07-30 14:53:16] Done. Check your files:
[INFO] [2020-07-30 14:53:16] (23 lines) /app/public/data/miller_pawson_mi/publish_nodes.tsv
[INFO] [2020-07-30 14:53:16] (25 lines) /app/public/data/miller_pawson_mi/publish_scientific_names.tsv
[INFO] [2020-07-30 14:53:16] (26 lines) /app/public/data/miller_pawson_mi/publish_traits.tsv
[INFO] [2020-07-30 14:53:16] (53 lines) /app/public/data/miller_pawson_mi/publish_metadata.tsv
[STOP] [2020-07-30 14:53:16] complete_harvest_instance
[START] [2020-07-30 14:53:16] completed
[STOP] [2020-07-30 14:53:16] completed
[STOP] [2020-07-30 14:53:16] logged process, took 97.18

Latest Process

30 Jul 14:51 EXITED currently processing 0