Harvest for Jordan 1992 Created 30 Jul 12:31

Harvesting Log

# Logfile created on 2020-07-30 12:30:02 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 12:30:02] logged process
[START] [2020-07-30 12:30:02] Creating resource from OpenData
[START] [2020-07-30 12:30:03] logged process
[START] [2020-07-30 12:30:03] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:30:03] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:30:03] Creating resource from OpenData
[INFO] [2020-07-30 12:30:19] ## HARVEST: type = -harvest
[START] [2020-07-30 12:30:43] logged process
[START] [2020-07-30 12:30:43] create_harvest_instance
[STOP] [2020-07-30 12:30:44] create_harvest_instance
[START] [2020-07-30 12:30:44] fetch_files
[STOP] [2020-07-30 12:30:44] fetch_files
[START] [2020-07-30 12:30:44] validate_each_file
[STOP] [2020-07-30 12:30:44] validate_each_file
[ERR] [2020-07-30 12:30:44] Exceptions::ColumnUnmatched
[ERR] [2020-07-30 12:30:44] TOO MANY COLUMNS: measurements: referenceID
[ERR] [2020-07-30 12:30:44] ../models/resource_harvester.rb:138:in `block in validate_each_file'
[ERR] [2020-07-30 12:30:44] ../models/resource_harvester.rb:665:in `block in each_format'
[ERR] [2020-07-30 12:30:44] ../models/resource_harvester.rb:650:in `each_format'
[ERR] [2020-07-30 12:30:44] ../models/resource_harvester.rb:132:in `validate_each_file'
[ERR] [2020-07-30 12:30:44] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2020-07-30 12:30:44] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-07-30 12:30:44] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2020-07-30 12:30:44] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2020-07-30 12:30:44] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2020-07-30 12:30:44] ../models/resource.rb:151:in `lock'
[ERR] [2020-07-30 12:30:44] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-07-30 12:30:44] ../models/resource.rb:232:in `harvest'
[ERR] [2020-07-30 12:30:44] bin/rails:4:in `require'
[ERR] [2020-07-30 12:30:44] bin/rails:4:in `<main>'
[STOP] [2020-07-30 12:30:44] logged process, took 1.39
[START] [2020-07-30 12:31:29] logged process
[START] [2020-07-30 12:31:29] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:31:29] Parse meta.xml file and create formats with fields
[INFO] [2020-07-30 12:31:49] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-07-30 12:31:49] ## remove_type: ScientificName
[INFO] [2020-07-30 12:31:49] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:31:49] [12:31:49.921] Removed 0 Scientificnames
[INFO] [2020-07-30 12:31:49] ## remove_type: Vernacular
[INFO] [2020-07-30 12:31:49] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:31:49] [12:31:49.924] Removed 0 Vernaculars
[INFO] [2020-07-30 12:31:49] ## remove_type: Article
[INFO] [2020-07-30 12:31:49] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:31:49] [12:31:49.928] Removed 0 Articles
[INFO] [2020-07-30 12:31:49] ## remove_type: Medium
[INFO] [2020-07-30 12:31:49] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:31:49] [12:31:49.932] Removed 0 Media
[INFO] [2020-07-30 12:31:49] ## remove_type: Trait
[INFO] [2020-07-30 12:31:49] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:31:49] [12:31:49.935] Removed 0 Traits
[INFO] [2020-07-30 12:31:49] ## remove_type: MetaTrait
[INFO] [2020-07-30 12:31:49] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:31:49] [12:31:49.939] Removed 0 Metatraits
[INFO] [2020-07-30 12:31:49] ## remove_type: OccurrenceMetadatum
[INFO] [2020-07-30 12:31:49] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:31:49] [12:31:49.942] Removed 0 Occurrencemetadata
[INFO] [2020-07-30 12:31:49] ## remove_type: Assoc
[INFO] [2020-07-30 12:31:49] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:31:49] [12:31:49.945] Removed 0 Assocs
[INFO] [2020-07-30 12:31:49] ## remove_type: MetaAssoc
[INFO] [2020-07-30 12:31:49] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:31:49] [12:31:49.947] Removed 0 Metaassocs
[INFO] [2020-07-30 12:31:49] ## remove_type: Identifier
[INFO] [2020-07-30 12:31:49] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:31:49] [12:31:49.949] Removed 0 Identifiers
[INFO] [2020-07-30 12:31:49] ## remove_type: Reference
[INFO] [2020-07-30 12:31:49] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:31:49] [12:31:49.952] Removed 0 References
[INFO] [2020-07-30 12:31:49] ## remove_type: Node
[INFO] [2020-07-30 12:31:49] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 12:31:49] [12:31:49.973] Removed 0 Nodes
[START] [2020-07-30 12:31:50] logged process
[START] [2020-07-30 12:31:50] Creating resource from OpenData
[START] [2020-07-30 12:31:50] logged process
[START] [2020-07-30 12:31:50] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:31:50] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:31:50] Creating resource from OpenData
[START] [2020-07-30 12:31:50] logged process
[START] [2020-07-30 12:31:50] create_harvest_instance
[STOP] [2020-07-30 12:31:52] create_harvest_instance
[START] [2020-07-30 12:31:52] fetch_files
[STOP] [2020-07-30 12:31:52] fetch_files
[START] [2020-07-30 12:31:52] validate_each_file
[STOP] [2020-07-30 12:31:52] validate_each_file
[START] [2020-07-30 12:31:52] convert_to_csv
[CMD] [2020-07-30 12:31:52] /usr/bin/sort /app/public/converted_csv/jordan_jordan_19_refs_22228.csv > /app/public/converted_csv/jordan_jordan_19_refs_22228.csv_sorted
[CMD] [2020-07-30 12:31:52] /usr/bin/sort /app/public/converted_csv/jordan_jordan_19_nodes_22229.csv > /app/public/converted_csv/jordan_jordan_19_nodes_22229.csv_sorted
[CMD] [2020-07-30 12:31:52] /usr/bin/sort /app/public/converted_csv/jordan_jordan_19_occurrences_22230.csv > /app/public/converted_csv/jordan_jordan_19_occurrences_22230.csv_sorted
[CMD] [2020-07-30 12:31:52] /usr/bin/sort /app/public/converted_csv/jordan_jordan_19_measurements_22231.csv > /app/public/converted_csv/jordan_jordan_19_measurements_22231.csv_sorted
[STOP] [2020-07-30 12:31:52] convert_to_csv
[START] [2020-07-30 12:31:52] calculate_delta
[CMD] [2020-07-30 12:31:52] echo "0a" > /app/public/diff/jordan_jordan_19_refs_22228.diff
[CMD] [2020-07-30 12:31:52] tail -n +1 /app/public/converted_csv/jordan_jordan_19_refs_22228.csv >> /app/public/diff/jordan_jordan_19_refs_22228.diff
[CMD] [2020-07-30 12:31:52] echo "." >> /app/public/diff/jordan_jordan_19_refs_22228.diff
[CMD] [2020-07-30 12:31:52] echo "0a" > /app/public/diff/jordan_jordan_19_nodes_22229.diff
[CMD] [2020-07-30 12:31:52] tail -n +1 /app/public/converted_csv/jordan_jordan_19_nodes_22229.csv >> /app/public/diff/jordan_jordan_19_nodes_22229.diff
[CMD] [2020-07-30 12:31:52] echo "." >> /app/public/diff/jordan_jordan_19_nodes_22229.diff
[CMD] [2020-07-30 12:31:52] echo "0a" > /app/public/diff/jordan_jordan_19_occurrences_22230.diff
[CMD] [2020-07-30 12:31:52] tail -n +1 /app/public/converted_csv/jordan_jordan_19_occurrences_22230.csv >> /app/public/diff/jordan_jordan_19_occurrences_22230.diff
[CMD] [2020-07-30 12:31:52] echo "." >> /app/public/diff/jordan_jordan_19_occurrences_22230.diff
[CMD] [2020-07-30 12:31:52] echo "0a" > /app/public/diff/jordan_jordan_19_measurements_22231.diff
[CMD] [2020-07-30 12:31:52] tail -n +1 /app/public/converted_csv/jordan_jordan_19_measurements_22231.csv >> /app/public/diff/jordan_jordan_19_measurements_22231.diff
[CMD] [2020-07-30 12:31:52] echo "." >> /app/public/diff/jordan_jordan_19_measurements_22231.diff
[STOP] [2020-07-30 12:31:52] calculate_delta
[START] [2020-07-30 12:31:52] parse_diff_and_store
[INFO] [2020-07-30 12:31:52] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 12:31:52] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 12:31:52] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 12:31:52] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 12:31:52] Storing 1 References
[INFO] [2020-07-30 12:31:52] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 12:31:52] Average Time: 0.01
[INFO] [2020-07-30 12:31:52] Total Time: 1s
[INFO] [2020-07-30 12:31:52] Storing 1 ScientificNames
[INFO] [2020-07-30 12:31:52] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 12:31:52] Average Time: 0.0
[INFO] [2020-07-30 12:31:52] Total Time: 1s
[INFO] [2020-07-30 12:31:52] Storing 1 Nodes
[INFO] [2020-07-30 12:31:52] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 12:31:52] Average Time: 0.0
[INFO] [2020-07-30 12:31:52] Total Time: 1s
[INFO] [2020-07-30 12:31:52] Storing 1 Occurrences
[INFO] [2020-07-30 12:31:52] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 12:31:52] Average Time: 0.0
[INFO] [2020-07-30 12:31:52] Total Time: 1s
[INFO] [2020-07-30 12:31:52] Storing 1 TraitsReferences
[INFO] [2020-07-30 12:31:52] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 12:31:52] Average Time: 0.03
[INFO] [2020-07-30 12:31:52] Total Time: 1s
[INFO] [2020-07-30 12:31:52] Storing 3 Traits
[INFO] [2020-07-30 12:31:52] Processing group of 3 in 1 groups of 1000
[INFO] [2020-07-30 12:31:52] Average Time: 0.0
[INFO] [2020-07-30 12:31:52] Total Time: 1s
[INFO] [2020-07-30 12:31:52] Storing 2 MetaTraits
[INFO] [2020-07-30 12:31:52] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 12:31:52] Average Time: 0.0
[INFO] [2020-07-30 12:31:52] Total Time: 1s
[STOP] [2020-07-30 12:31:52] parse_diff_and_store
[START] [2020-07-30 12:31:52] resolve_keys
[INFO] [2020-07-30 12:31:59] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 12:31:59] traits to occurrences...
[INFO] [2020-07-30 12:31:59] traits to nodes (through occurrences)...
[INFO] [2020-07-30 12:31:59] Traits to sex term...
[INFO] [2020-07-30 12:31:59] Traits to lifestage term...
[INFO] [2020-07-30 12:31:59] MetaTraits to traits...
[INFO] [2020-07-30 12:31:59] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 12:31:59] Assocs to occurrences...
[INFO] [2020-07-30 12:31:59] Assocs to nodes...
[INFO] [2020-07-30 12:31:59] Assoc to sex term...
[INFO] [2020-07-30 12:31:59] Assoc to lifestage term...
[STOP] [2020-07-30 12:31:59] resolve_keys
[START] [2020-07-30 12:31:59] hold_for_later_1
[STOP] [2020-07-30 12:31:59] hold_for_later_1
[START] [2020-07-30 12:31:59] hold_for_later_2
[STOP] [2020-07-30 12:31:59] hold_for_later_2
[START] [2020-07-30 12:31:59] resolve_missing_parents
[STOP] [2020-07-30 12:31:59] resolve_missing_parents
[START] [2020-07-30 12:31:59] rebuild_nodes
[START] [2020-07-30 12:31:59] Flattener#flatten
[START] [2020-07-30 12:31:59] Flattener#study_resource
[START] [2020-07-30 12:31:59] Flattener#build_ancestry
[STOP] [2020-07-30 12:31:59] Flattener#build_ancestry
[INFO] [2020-07-30 12:31:59] 1 ancestry keys
[START] [2020-07-30 12:31:59] build_node_ancestors
[INFO] [2020-07-30 12:31:59] old ancestors deleted.
[STOP] [2020-07-30 12:31:59] build_node_ancestors
[WARN] [2020-07-30 12:31:59] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 12:31:59] Flattener#flatten
[STOP] [2020-07-30 12:31:59] rebuild_nodes
[START] [2020-07-30 12:31:59] resolve_missing_media_owners
[STOP] [2020-07-30 12:31:59] resolve_missing_media_owners
[START] [2020-07-30 12:31:59] sanitize_media_verbatims
[STOP] [2020-07-30 12:31:59] sanitize_media_verbatims
[START] [2020-07-30 12:31:59] queue_downloads
[STOP] [2020-07-30 12:31:59] queue_downloads
[START] [2020-07-30 12:31:59] parse_names
[WARN] [2020-07-30 12:31:59] I see 1 names which still need to be parsed.
[STOP] [2020-07-30 12:32:01] parse_names
[START] [2020-07-30 12:32:01] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 12:32:01] denormalize_canonical_names_to_nodes
[START] [2020-07-30 12:32:01] match_nodes
[START] [2020-07-30 12:32:01] map_all_nodes_to_pages
[STOP] [2020-07-30 12:32:01] map_all_nodes_to_pages
[INFO] [2020-07-30 12:32:01] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-07-30 12:32:01] update_nodes
[STOP] [2020-07-30 12:32:01] update_nodes
[STOP] [2020-07-30 12:32:01] match_nodes
[START] [2020-07-30 12:32:01] reindex_search
[STOP] [2020-07-30 12:32:01] reindex_search
[START] [2020-07-30 12:32:01] normalize_units
[STOP] [2020-07-30 12:32:01] normalize_units
[START] [2020-07-30 12:32:01] calculate_statistics
[2020-07-30 12:32:01] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 12:32:01] calculate_statistics
[START] [2020-07-30 12:32:01] complete_harvest_instance
[START] [2020-07-30 12:32:01] overall_tsv_creation
[INFO] [2020-07-30 12:32:01] Processing group of 1 in 1 batches of 10000
[INFO] [2020-07-30 12:32:49] 1 Traits (unfiltered)...
[INFO] [2020-07-30 12:33:24] 1 Traits (filtered)...
[INFO] [2020-07-30 12:33:24] 0 Associations (filtered)...
[INFO] [2020-07-30 12:33:24] 5 metadata added.
[INFO] [2020-07-30 12:33:24] 0 metadata added.
[INFO] [2020-07-30 12:33:24] Average Time: 56.34
[INFO] [2020-07-30 12:33:24] Total Time: 1m24s
[STOP] [2020-07-30 12:33:24] overall_tsv_creation
[INFO] [2020-07-30 12:33:24] Done. Check your files:
[INFO] [2020-07-30 12:33:24] (1 lines) /app/public/data/jordan_jordan_19/publish_nodes.tsv
[INFO] [2020-07-30 12:33:24] (1 lines) /app/public/data/jordan_jordan_19/publish_scientific_names.tsv
[INFO] [2020-07-30 12:33:24] (2 lines) /app/public/data/jordan_jordan_19/publish_traits.tsv
[INFO] [2020-07-30 12:33:24] (4 lines) /app/public/data/jordan_jordan_19/publish_metadata.tsv
[STOP] [2020-07-30 12:33:24] complete_harvest_instance
[START] [2020-07-30 12:33:24] completed
[STOP] [2020-07-30 12:33:24] completed
[STOP] [2020-07-30 12:33:24] logged process, took 94.05

Latest Process

30 Jul 12:31 EXITED currently processing 0