Harvest for Kristan 2019 Created 30 Jul 12:47

Harvesting Log

# Logfile created on 2020-07-30 12:35:25 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 12:35:25] logged process
[START] [2020-07-30 12:35:25] Creating resource from OpenData
[START] [2020-07-30 12:35:25] logged process
[START] [2020-07-30 12:35:25] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:35:25] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:35:25] Creating resource from OpenData
[INFO] [2020-07-30 12:46:49] ## HARVEST: type = -harvest
[START] [2020-07-30 12:46:53] logged process
[START] [2020-07-30 12:46:53] create_harvest_instance
[STOP] [2020-07-30 12:46:54] create_harvest_instance
[START] [2020-07-30 12:46:54] fetch_files
[STOP] [2020-07-30 12:46:54] fetch_files
[START] [2020-07-30 12:46:54] validate_each_file
[STOP] [2020-07-30 12:46:54] validate_each_file
[ERR] [2020-07-30 12:46:54] Exceptions::ColumnUnmatched
[ERR] [2020-07-30 12:46:54] TOO MANY COLUMNS: measurements: referenceID
[ERR] [2020-07-30 12:46:54] ../models/resource_harvester.rb:138:in `block in validate_each_file'
[ERR] [2020-07-30 12:46:54] ../models/resource_harvester.rb:665:in `block in each_format'
[ERR] [2020-07-30 12:46:54] ../models/resource_harvester.rb:650:in `each_format'
[ERR] [2020-07-30 12:46:54] ../models/resource_harvester.rb:132:in `validate_each_file'
[ERR] [2020-07-30 12:46:54] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2020-07-30 12:46:54] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-07-30 12:46:54] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2020-07-30 12:46:54] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2020-07-30 12:46:54] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2020-07-30 12:46:54] ../models/resource.rb:151:in `lock'
[ERR] [2020-07-30 12:46:54] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-07-30 12:46:54] ../models/resource.rb:232:in `harvest'
[ERR] [2020-07-30 12:46:54] bin/rails:4:in `require'
[ERR] [2020-07-30 12:46:54] bin/rails:4:in `<main>'
[STOP] [2020-07-30 12:46:54] logged process, took 1.43
[INFO] [2020-07-30 12:47:27] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-07-30 12:47:31] ## remove_type: ScientificName
[INFO] [2020-07-30 12:47:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:47:31] [12:47:31.151] Removed 0 Scientificnames
[INFO] [2020-07-30 12:47:31] ## remove_type: Vernacular
[INFO] [2020-07-30 12:47:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:47:31] [12:47:31.154] Removed 0 Vernaculars
[INFO] [2020-07-30 12:47:31] ## remove_type: Article
[INFO] [2020-07-30 12:47:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:47:31] [12:47:31.157] Removed 0 Articles
[INFO] [2020-07-30 12:47:31] ## remove_type: Medium
[INFO] [2020-07-30 12:47:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:47:31] [12:47:31.160] Removed 0 Media
[INFO] [2020-07-30 12:47:31] ## remove_type: Trait
[INFO] [2020-07-30 12:47:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:47:31] [12:47:31.164] Removed 0 Traits
[INFO] [2020-07-30 12:47:31] ## remove_type: MetaTrait
[INFO] [2020-07-30 12:47:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:47:31] [12:47:31.166] Removed 0 Metatraits
[INFO] [2020-07-30 12:47:31] ## remove_type: OccurrenceMetadatum
[INFO] [2020-07-30 12:47:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:47:31] [12:47:31.169] Removed 0 Occurrencemetadata
[INFO] [2020-07-30 12:47:31] ## remove_type: Assoc
[INFO] [2020-07-30 12:47:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:47:31] [12:47:31.172] Removed 0 Assocs
[INFO] [2020-07-30 12:47:31] ## remove_type: MetaAssoc
[INFO] [2020-07-30 12:47:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:47:31] [12:47:31.175] Removed 0 Metaassocs
[INFO] [2020-07-30 12:47:31] ## remove_type: Identifier
[INFO] [2020-07-30 12:47:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:47:31] [12:47:31.177] Removed 0 Identifiers
[INFO] [2020-07-30 12:47:31] ## remove_type: Reference
[INFO] [2020-07-30 12:47:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:47:31] [12:47:31.180] Removed 0 References
[INFO] [2020-07-30 12:47:31] ## remove_type: Node
[INFO] [2020-07-30 12:47:31] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:47:31] [12:47:31.200] Removed 0 Nodes
[START] [2020-07-30 12:47:31] logged process
[START] [2020-07-30 12:47:31] Creating resource from OpenData
[START] [2020-07-30 12:47:31] logged process
[START] [2020-07-30 12:47:31] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:47:31] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:47:31] Creating resource from OpenData
[START] [2020-07-30 12:47:31] logged process
[START] [2020-07-30 12:47:31] create_harvest_instance
[STOP] [2020-07-30 12:47:33] create_harvest_instance
[START] [2020-07-30 12:47:33] fetch_files
[STOP] [2020-07-30 12:47:33] fetch_files
[START] [2020-07-30 12:47:33] validate_each_file
[STOP] [2020-07-30 12:47:33] validate_each_file
[START] [2020-07-30 12:47:33] convert_to_csv
[CMD] [2020-07-30 12:47:33] /usr/bin/sort /app/public/converted_csv/kristan_kristan__refs_22252.csv > /app/public/converted_csv/kristan_kristan__refs_22252.csv_sorted
[CMD] [2020-07-30 12:47:33] /usr/bin/sort /app/public/converted_csv/kristan_kristan__nodes_22253.csv > /app/public/converted_csv/kristan_kristan__nodes_22253.csv_sorted
[CMD] [2020-07-30 12:47:33] /usr/bin/sort /app/public/converted_csv/kristan_kristan__occurrences_22254.csv > /app/public/converted_csv/kristan_kristan__occurrences_22254.csv_sorted
[CMD] [2020-07-30 12:47:33] /usr/bin/sort /app/public/converted_csv/kristan_kristan__measurements_22255.csv > /app/public/converted_csv/kristan_kristan__measurements_22255.csv_sorted
[STOP] [2020-07-30 12:47:33] convert_to_csv
[START] [2020-07-30 12:47:33] calculate_delta
[CMD] [2020-07-30 12:47:33] echo "0a" > /app/public/diff/kristan_kristan__refs_22252.diff
[CMD] [2020-07-30 12:47:33] tail -n +1 /app/public/converted_csv/kristan_kristan__refs_22252.csv >> /app/public/diff/kristan_kristan__refs_22252.diff
[CMD] [2020-07-30 12:47:33] echo "." >> /app/public/diff/kristan_kristan__refs_22252.diff
[CMD] [2020-07-30 12:47:33] echo "0a" > /app/public/diff/kristan_kristan__nodes_22253.diff
[CMD] [2020-07-30 12:47:33] tail -n +1 /app/public/converted_csv/kristan_kristan__nodes_22253.csv >> /app/public/diff/kristan_kristan__nodes_22253.diff
[CMD] [2020-07-30 12:47:33] echo "." >> /app/public/diff/kristan_kristan__nodes_22253.diff
[CMD] [2020-07-30 12:47:33] echo "0a" > /app/public/diff/kristan_kristan__occurrences_22254.diff
[CMD] [2020-07-30 12:47:33] tail -n +1 /app/public/converted_csv/kristan_kristan__occurrences_22254.csv >> /app/public/diff/kristan_kristan__occurrences_22254.diff
[CMD] [2020-07-30 12:47:33] echo "." >> /app/public/diff/kristan_kristan__occurrences_22254.diff
[CMD] [2020-07-30 12:47:33] echo "0a" > /app/public/diff/kristan_kristan__measurements_22255.diff
[CMD] [2020-07-30 12:47:33] tail -n +1 /app/public/converted_csv/kristan_kristan__measurements_22255.csv >> /app/public/diff/kristan_kristan__measurements_22255.diff
[CMD] [2020-07-30 12:47:33] echo "." >> /app/public/diff/kristan_kristan__measurements_22255.diff
[STOP] [2020-07-30 12:47:33] calculate_delta
[START] [2020-07-30 12:47:33] parse_diff_and_store
[INFO] [2020-07-30 12:47:33] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 12:47:33] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 12:47:33] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 12:47:33] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 12:47:33] Storing 2 References
[INFO] [2020-07-30 12:47:33] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 12:47:33] Average Time: 0.0
[INFO] [2020-07-30 12:47:33] Total Time: 1s
[INFO] [2020-07-30 12:47:33] Storing 5 ScientificNames
[INFO] [2020-07-30 12:47:33] Processing group of 5 in 1 groups of 1000
[INFO] [2020-07-30 12:47:33] Average Time: 0.0
[INFO] [2020-07-30 12:47:33] Total Time: 1s
[INFO] [2020-07-30 12:47:33] Storing 5 Nodes
[INFO] [2020-07-30 12:47:33] Processing group of 5 in 1 groups of 1000
[INFO] [2020-07-30 12:47:33] Average Time: 0.0
[INFO] [2020-07-30 12:47:33] Total Time: 1s
[INFO] [2020-07-30 12:47:33] Storing 5 Occurrences
[INFO] [2020-07-30 12:47:33] Processing group of 5 in 1 groups of 1000
[INFO] [2020-07-30 12:47:33] Average Time: 0.0
[INFO] [2020-07-30 12:47:33] Total Time: 1s
[INFO] [2020-07-30 12:47:33] Storing 4 TraitsReferences
[INFO] [2020-07-30 12:47:33] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 12:47:33] Average Time: 0.0
[INFO] [2020-07-30 12:47:33] Total Time: 1s
[INFO] [2020-07-30 12:47:33] Storing 17 Traits
[INFO] [2020-07-30 12:47:33] Processing group of 17 in 1 groups of 1000
[INFO] [2020-07-30 12:47:33] Average Time: 0.01
[INFO] [2020-07-30 12:47:33] Total Time: 1s
[INFO] [2020-07-30 12:47:33] Storing 18 MetaTraits
[INFO] [2020-07-30 12:47:33] Processing group of 18 in 1 groups of 1000
[INFO] [2020-07-30 12:47:33] Average Time: 0.0
[INFO] [2020-07-30 12:47:33] Total Time: 1s
[STOP] [2020-07-30 12:47:33] parse_diff_and_store
[START] [2020-07-30 12:47:33] resolve_keys
[INFO] [2020-07-30 12:47:40] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 12:47:40] traits to occurrences...
[INFO] [2020-07-30 12:47:40] traits to nodes (through occurrences)...
[INFO] [2020-07-30 12:47:40] Traits to sex term...
[INFO] [2020-07-30 12:47:40] Traits to lifestage term...
[INFO] [2020-07-30 12:47:40] MetaTraits to traits...
[INFO] [2020-07-30 12:47:40] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 12:47:40] Assocs to occurrences...
[INFO] [2020-07-30 12:47:40] Assocs to nodes...
[INFO] [2020-07-30 12:47:40] Assoc to sex term...
[INFO] [2020-07-30 12:47:40] Assoc to lifestage term...
[STOP] [2020-07-30 12:47:40] resolve_keys
[START] [2020-07-30 12:47:40] hold_for_later_1
[STOP] [2020-07-30 12:47:40] hold_for_later_1
[START] [2020-07-30 12:47:40] hold_for_later_2
[STOP] [2020-07-30 12:47:40] hold_for_later_2
[START] [2020-07-30 12:47:40] resolve_missing_parents
[STOP] [2020-07-30 12:47:40] resolve_missing_parents
[START] [2020-07-30 12:47:40] rebuild_nodes
[START] [2020-07-30 12:47:40] Flattener#flatten
[START] [2020-07-30 12:47:40] Flattener#study_resource
[START] [2020-07-30 12:47:40] Flattener#build_ancestry
[STOP] [2020-07-30 12:47:40] Flattener#build_ancestry
[INFO] [2020-07-30 12:47:40] 5 ancestry keys
[START] [2020-07-30 12:47:40] build_node_ancestors
[INFO] [2020-07-30 12:47:40] old ancestors deleted.
[STOP] [2020-07-30 12:47:40] build_node_ancestors
[WARN] [2020-07-30 12:47:40] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 12:47:40] Flattener#flatten
[STOP] [2020-07-30 12:47:40] rebuild_nodes
[START] [2020-07-30 12:47:40] resolve_missing_media_owners
[STOP] [2020-07-30 12:47:40] resolve_missing_media_owners
[START] [2020-07-30 12:47:40] sanitize_media_verbatims
[STOP] [2020-07-30 12:47:40] sanitize_media_verbatims
[START] [2020-07-30 12:47:40] queue_downloads
[STOP] [2020-07-30 12:47:40] queue_downloads
[START] [2020-07-30 12:47:40] parse_names
[WARN] [2020-07-30 12:47:40] I see 5 names which still need to be parsed.
[STOP] [2020-07-30 12:47:41] parse_names
[START] [2020-07-30 12:47:41] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 12:47:41] denormalize_canonical_names_to_nodes
[START] [2020-07-30 12:47:41] match_nodes
[START] [2020-07-30 12:47:41] map_all_nodes_to_pages
[STOP] [2020-07-30 12:47:43] map_all_nodes_to_pages
[INFO] [2020-07-30 12:47:43] ZERO unmatched nodes (of 5)! Nicely done.
[START] [2020-07-30 12:47:43] update_nodes
[STOP] [2020-07-30 12:47:43] update_nodes
[STOP] [2020-07-30 12:47:43] match_nodes
[START] [2020-07-30 12:47:43] reindex_search
[STOP] [2020-07-30 12:47:43] reindex_search
[START] [2020-07-30 12:47:43] normalize_units
[STOP] [2020-07-30 12:47:43] normalize_units
[START] [2020-07-30 12:47:43] calculate_statistics
[2020-07-30 12:47:43] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 12:47:43] calculate_statistics
[START] [2020-07-30 12:47:43] complete_harvest_instance
[START] [2020-07-30 12:47:43] overall_tsv_creation
[INFO] [2020-07-30 12:47:43] Processing group of 5 in 1 batches of 10000
[INFO] [2020-07-30 12:48:32] 8 Traits (unfiltered)...
[INFO] [2020-07-30 12:49:08] 8 Traits (filtered)...
[INFO] [2020-07-30 12:49:08] 0 Associations (filtered)...
[INFO] [2020-07-30 12:49:08] 31 metadata added.
[INFO] [2020-07-30 12:49:08] 0 metadata added.
[INFO] [2020-07-30 12:49:08] Average Time: 57.83
[INFO] [2020-07-30 12:49:08] Total Time: 1m25s
[STOP] [2020-07-30 12:49:08] overall_tsv_creation
[INFO] [2020-07-30 12:49:08] Done. Check your files:
[INFO] [2020-07-30 12:49:08] (5 lines) /app/public/data/kristan_kristan_/publish_nodes.tsv
[INFO] [2020-07-30 12:49:08] (5 lines) /app/public/data/kristan_kristan_/publish_scientific_names.tsv
[INFO] [2020-07-30 12:49:08] (9 lines) /app/public/data/kristan_kristan_/publish_traits.tsv
[INFO] [2020-07-30 12:49:08] (14 lines) /app/public/data/kristan_kristan_/publish_metadata.tsv
[STOP] [2020-07-30 12:49:08] complete_harvest_instance
[START] [2020-07-30 12:49:08] completed
[STOP] [2020-07-30 12:49:08] completed
[STOP] [2020-07-30 12:49:08] logged process, took 96.79

Latest Process

30 Jul 12:47 EXITED currently processing 0