Harvest for Kretschmar and Baumann 1999 Created 11 Jun 13:26

Harvesting Log

# Logfile created on 2020-06-11 13:15:02 -0400 by logger.rb/v1.4.2
[INFO] [2020-06-11 13:15:03] ## HARVEST: type = -harvest
[START] [2020-06-11 13:15:04] logged process
[START] [2020-06-11 13:15:04] create_harvest_instance
[STOP] [2020-06-11 13:15:04] create_harvest_instance
[ERR] [2020-06-11 13:15:04] NoMethodError
[ERR] [2020-06-11 13:15:04] undefined method `fields' for nil:NilClass
[ERR] [2020-06-11 13:15:04] ../models/resource.rb:277:in `create_harvest_instance'
[ERR] [2020-06-11 13:15:04] ../models/resource_harvester.rb:108:in `create_harvest_instance'
[ERR] [2020-06-11 13:15:04] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2020-06-11 13:15:04] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-06-11 13:15:04] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2020-06-11 13:15:04] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2020-06-11 13:15:04] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2020-06-11 13:15:04] ../models/resource.rb:151:in `lock'
[ERR] [2020-06-11 13:15:04] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-06-11 13:15:04] ../models/resource.rb:232:in `harvest'
[ERR] [2020-06-11 13:15:04] bin/rails:4:in `require'
[ERR] [2020-06-11 13:15:04] bin/rails:4:in `<main>'
[STOP] [2020-06-11 13:15:04] logged process, took 0.06
[INFO] [2020-06-11 13:16:59] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-11 13:17:02] ## remove_type: ScientificName
[INFO] [2020-06-11 13:17:02] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:17:02] [13:17:02.626] Removed 0 Scientificnames
[INFO] [2020-06-11 13:17:02] ## remove_type: Vernacular
[INFO] [2020-06-11 13:17:02] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:17:02] [13:17:02.629] Removed 0 Vernaculars
[INFO] [2020-06-11 13:17:02] ## remove_type: Article
[INFO] [2020-06-11 13:17:02] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:17:02] [13:17:02.632] Removed 0 Articles
[INFO] [2020-06-11 13:17:02] ## remove_type: Medium
[INFO] [2020-06-11 13:17:02] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:17:02] [13:17:02.636] Removed 0 Media
[INFO] [2020-06-11 13:17:02] ## remove_type: Trait
[INFO] [2020-06-11 13:17:02] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:17:02] [13:17:02.639] Removed 0 Traits
[INFO] [2020-06-11 13:17:02] ## remove_type: MetaTrait
[INFO] [2020-06-11 13:17:02] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:17:02] [13:17:02.642] Removed 0 Metatraits
[INFO] [2020-06-11 13:17:02] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-11 13:17:02] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:17:02] [13:17:02.645] Removed 0 Occurrencemetadata
[INFO] [2020-06-11 13:17:02] ## remove_type: Assoc
[INFO] [2020-06-11 13:17:02] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:17:02] [13:17:02.648] Removed 0 Assocs
[INFO] [2020-06-11 13:17:02] ## remove_type: MetaAssoc
[INFO] [2020-06-11 13:17:02] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:17:02] [13:17:02.650] Removed 0 Metaassocs
[INFO] [2020-06-11 13:17:02] ## remove_type: Identifier
[INFO] [2020-06-11 13:17:02] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:17:02] [13:17:02.653] Removed 0 Identifiers
[INFO] [2020-06-11 13:17:02] ## remove_type: Reference
[INFO] [2020-06-11 13:17:02] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:17:02] [13:17:02.656] Removed 0 References
[INFO] [2020-06-11 13:17:02] ## remove_type: Node
[INFO] [2020-06-11 13:17:02] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:17:02] [13:17:02.688] Removed 0 Nodes
[START] [2020-06-11 13:17:02] logged process
[START] [2020-06-11 13:17:02] Creating resource from OpenData
[START] [2020-06-11 13:17:03] logged process
[START] [2020-06-11 13:17:03] Parse meta.xml file and create formats with fields
[WARN] [2020-06-11 13:17:03] SKIPPING missing file: /app/public/data/kretschmar_bauma/taxa.tsv
[WARN] [2020-06-11 13:17:03] SKIPPING missing file: /app/public/data/kretschmar_bauma/occurrences.tsv
[WARN] [2020-06-11 13:17:03] SKIPPING missing file: /app/public/data/kretschmar_bauma/measurementsorfacts.tsv
[STOP] [2020-06-11 13:17:03] Parse meta.xml file and create formats with fields
[STOP] [2020-06-11 13:17:03] Creating resource from OpenData
[START] [2020-06-11 13:17:03] logged process
[START] [2020-06-11 13:17:03] create_harvest_instance
[STOP] [2020-06-11 13:17:03] create_harvest_instance
[ERR] [2020-06-11 13:17:03] NoMethodError
[ERR] [2020-06-11 13:17:03] undefined method `fields' for nil:NilClass
[ERR] [2020-06-11 13:17:03] ../models/resource.rb:277:in `create_harvest_instance'
[ERR] [2020-06-11 13:17:03] ../models/resource_harvester.rb:108:in `create_harvest_instance'
[ERR] [2020-06-11 13:17:03] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2020-06-11 13:17:03] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-06-11 13:17:03] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2020-06-11 13:17:03] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2020-06-11 13:17:03] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2020-06-11 13:17:03] ../models/resource.rb:151:in `lock'
[ERR] [2020-06-11 13:17:03] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-06-11 13:17:03] ../models/resource.rb:232:in `harvest'
[ERR] [2020-06-11 13:17:03] ../models/resource.rb:208:in `re_download_opendata_and_harvest'
[ERR] [2020-06-11 13:17:03] bin/rails:4:in `require'
[ERR] [2020-06-11 13:17:03] bin/rails:4:in `<main>'
[STOP] [2020-06-11 13:17:03] logged process, took 0.02
[INFO] [2020-06-11 13:26:13] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-11 13:26:14] ## remove_type: ScientificName
[INFO] [2020-06-11 13:26:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:26:14] [13:26:14.355] Removed 0 Scientificnames
[INFO] [2020-06-11 13:26:14] ## remove_type: Vernacular
[INFO] [2020-06-11 13:26:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:26:14] [13:26:14.358] Removed 0 Vernaculars
[INFO] [2020-06-11 13:26:14] ## remove_type: Article
[INFO] [2020-06-11 13:26:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:26:14] [13:26:14.361] Removed 0 Articles
[INFO] [2020-06-11 13:26:14] ## remove_type: Medium
[INFO] [2020-06-11 13:26:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:26:14] [13:26:14.364] Removed 0 Media
[INFO] [2020-06-11 13:26:14] ## remove_type: Trait
[INFO] [2020-06-11 13:26:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:26:14] [13:26:14.368] Removed 0 Traits
[INFO] [2020-06-11 13:26:14] ## remove_type: MetaTrait
[INFO] [2020-06-11 13:26:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:26:14] [13:26:14.371] Removed 0 Metatraits
[INFO] [2020-06-11 13:26:14] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-11 13:26:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:26:14] [13:26:14.373] Removed 0 Occurrencemetadata
[INFO] [2020-06-11 13:26:14] ## remove_type: Assoc
[INFO] [2020-06-11 13:26:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:26:14] [13:26:14.376] Removed 0 Assocs
[INFO] [2020-06-11 13:26:14] ## remove_type: MetaAssoc
[INFO] [2020-06-11 13:26:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:26:14] [13:26:14.379] Removed 0 Metaassocs
[INFO] [2020-06-11 13:26:14] ## remove_type: Identifier
[INFO] [2020-06-11 13:26:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:26:14] [13:26:14.381] Removed 0 Identifiers
[INFO] [2020-06-11 13:26:14] ## remove_type: Reference
[INFO] [2020-06-11 13:26:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:26:14] [13:26:14.384] Removed 0 References
[INFO] [2020-06-11 13:26:14] ## remove_type: Node
[INFO] [2020-06-11 13:26:14] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:26:14] [13:26:14.404] Removed 0 Nodes
[START] [2020-06-11 13:26:14] logged process
[START] [2020-06-11 13:26:14] Creating resource from OpenData
[START] [2020-06-11 13:26:14] logged process
[START] [2020-06-11 13:26:14] Parse meta.xml file and create formats with fields
[STOP] [2020-06-11 13:26:14] Parse meta.xml file and create formats with fields
[STOP] [2020-06-11 13:26:14] Creating resource from OpenData
[START] [2020-06-11 13:26:14] logged process
[START] [2020-06-11 13:26:14] create_harvest_instance
[STOP] [2020-06-11 13:26:15] create_harvest_instance
[START] [2020-06-11 13:26:15] fetch_files
[STOP] [2020-06-11 13:26:15] fetch_files
[START] [2020-06-11 13:26:15] validate_each_file
[STOP] [2020-06-11 13:26:16] validate_each_file
[START] [2020-06-11 13:26:16] convert_to_csv
[CMD] [2020-06-11 13:26:16] /usr/bin/sort /app/public/converted_csv/kretschmar_bauma_nodes_21141.csv > /app/public/converted_csv/kretschmar_bauma_nodes_21141.csv_sorted
[CMD] [2020-06-11 13:26:16] /usr/bin/sort /app/public/converted_csv/kretschmar_bauma_occurrences_21142.csv > /app/public/converted_csv/kretschmar_bauma_occurrences_21142.csv_sorted
[CMD] [2020-06-11 13:26:16] /usr/bin/sort /app/public/converted_csv/kretschmar_bauma_measurements_21143.csv > /app/public/converted_csv/kretschmar_bauma_measurements_21143.csv_sorted
[STOP] [2020-06-11 13:26:16] convert_to_csv
[START] [2020-06-11 13:26:16] calculate_delta
[CMD] [2020-06-11 13:26:16] echo "0a" > /app/public/diff/kretschmar_bauma_nodes_21141.diff
[CMD] [2020-06-11 13:26:16] tail -n +1 /app/public/converted_csv/kretschmar_bauma_nodes_21141.csv >> /app/public/diff/kretschmar_bauma_nodes_21141.diff
[CMD] [2020-06-11 13:26:16] echo "." >> /app/public/diff/kretschmar_bauma_nodes_21141.diff
[CMD] [2020-06-11 13:26:16] echo "0a" > /app/public/diff/kretschmar_bauma_occurrences_21142.diff
[CMD] [2020-06-11 13:26:16] tail -n +1 /app/public/converted_csv/kretschmar_bauma_occurrences_21142.csv >> /app/public/diff/kretschmar_bauma_occurrences_21142.diff
[CMD] [2020-06-11 13:26:16] echo "." >> /app/public/diff/kretschmar_bauma_occurrences_21142.diff
[CMD] [2020-06-11 13:26:16] echo "0a" > /app/public/diff/kretschmar_bauma_measurements_21143.diff
[CMD] [2020-06-11 13:26:16] tail -n +1 /app/public/converted_csv/kretschmar_bauma_measurements_21143.csv >> /app/public/diff/kretschmar_bauma_measurements_21143.diff
[CMD] [2020-06-11 13:26:16] echo "." >> /app/public/diff/kretschmar_bauma_measurements_21143.diff
[STOP] [2020-06-11 13:26:16] calculate_delta
[START] [2020-06-11 13:26:16] parse_diff_and_store
[INFO] [2020-06-11 13:26:16] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-11 13:26:16] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-11 13:26:16] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-11 13:26:16] Storing 8 ScientificNames
[INFO] [2020-06-11 13:26:16] Processing group of 8 in 1 groups of 1000
[INFO] [2020-06-11 13:26:16] Average Time: 0.0
[INFO] [2020-06-11 13:26:16] Total Time: 1s
[INFO] [2020-06-11 13:26:16] Storing 8 Nodes
[INFO] [2020-06-11 13:26:16] Processing group of 8 in 1 groups of 1000
[INFO] [2020-06-11 13:26:16] Average Time: 0.0
[INFO] [2020-06-11 13:26:16] Total Time: 1s
[INFO] [2020-06-11 13:26:16] Storing 5 Occurrences
[INFO] [2020-06-11 13:26:16] Processing group of 5 in 1 groups of 1000
[INFO] [2020-06-11 13:26:16] Average Time: 0.0
[INFO] [2020-06-11 13:26:16] Total Time: 1s
[INFO] [2020-06-11 13:26:16] Storing 36 Traits
[INFO] [2020-06-11 13:26:16] Processing group of 36 in 1 groups of 1000
[INFO] [2020-06-11 13:26:16] Average Time: 0.02
[INFO] [2020-06-11 13:26:16] Total Time: 1s
[INFO] [2020-06-11 13:26:16] Storing 42 MetaTraits
[INFO] [2020-06-11 13:26:16] Processing group of 42 in 1 groups of 1000
[INFO] [2020-06-11 13:26:16] Average Time: 0.01
[INFO] [2020-06-11 13:26:16] Total Time: 1s
[STOP] [2020-06-11 13:26:16] parse_diff_and_store
[START] [2020-06-11 13:26:16] resolve_keys
[INFO] [2020-06-11 13:26:23] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-11 13:26:23] traits to occurrences...
[INFO] [2020-06-11 13:26:23] traits to nodes (through occurrences)...
[INFO] [2020-06-11 13:26:23] Traits to sex term...
[INFO] [2020-06-11 13:26:23] Traits to lifestage term...
[INFO] [2020-06-11 13:26:23] MetaTraits to traits...
[INFO] [2020-06-11 13:26:23] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-11 13:26:23] Assocs to occurrences...
[INFO] [2020-06-11 13:26:23] Assocs to nodes...
[INFO] [2020-06-11 13:26:23] Assoc to sex term...
[INFO] [2020-06-11 13:26:23] Assoc to lifestage term...
[STOP] [2020-06-11 13:26:23] resolve_keys
[START] [2020-06-11 13:26:23] hold_for_later_1
[STOP] [2020-06-11 13:26:23] hold_for_later_1
[START] [2020-06-11 13:26:23] hold_for_later_2
[STOP] [2020-06-11 13:26:23] hold_for_later_2
[START] [2020-06-11 13:26:23] resolve_missing_parents
[STOP] [2020-06-11 13:26:23] resolve_missing_parents
[START] [2020-06-11 13:26:23] rebuild_nodes
[START] [2020-06-11 13:26:23] Flattener#flatten
[START] [2020-06-11 13:26:23] Flattener#study_resource
[START] [2020-06-11 13:26:23] Flattener#build_ancestry
[STOP] [2020-06-11 13:26:23] Flattener#build_ancestry
[INFO] [2020-06-11 13:26:23] 8 ancestry keys
[START] [2020-06-11 13:26:23] build_node_ancestors
[INFO] [2020-06-11 13:26:23] old ancestors deleted.
[STOP] [2020-06-11 13:26:23] build_node_ancestors
[START] [2020-06-11 13:26:23] Flattener#propagate_ancestor_ids
[STOP] [2020-06-11 13:26:23] Flattener#propagate_ancestor_ids
[STOP] [2020-06-11 13:26:23] Flattener#flatten
[STOP] [2020-06-11 13:26:23] rebuild_nodes
[START] [2020-06-11 13:26:23] resolve_missing_media_owners
[STOP] [2020-06-11 13:26:23] resolve_missing_media_owners
[START] [2020-06-11 13:26:23] sanitize_media_verbatims
[STOP] [2020-06-11 13:26:23] sanitize_media_verbatims
[START] [2020-06-11 13:26:23] queue_downloads
[STOP] [2020-06-11 13:26:23] queue_downloads
[START] [2020-06-11 13:26:23] parse_names
[WARN] [2020-06-11 13:26:23] I see 8 names which still need to be parsed.
[STOP] [2020-06-11 13:26:24] parse_names
[START] [2020-06-11 13:26:24] denormalize_canonical_names_to_nodes
[STOP] [2020-06-11 13:26:24] denormalize_canonical_names_to_nodes
[START] [2020-06-11 13:26:24] match_nodes
[START] [2020-06-11 13:26:24] map_all_nodes_to_pages
[STOP] [2020-06-11 13:26:25] map_all_nodes_to_pages
[INFO] [2020-06-11 13:26:25] ZERO unmatched nodes (of 8)! Nicely done.
[START] [2020-06-11 13:26:25] update_nodes
[STOP] [2020-06-11 13:26:25] update_nodes
[STOP] [2020-06-11 13:26:25] match_nodes
[START] [2020-06-11 13:26:25] reindex_search
[STOP] [2020-06-11 13:26:25] reindex_search
[START] [2020-06-11 13:26:25] normalize_units
[STOP] [2020-06-11 13:26:25] normalize_units
[START] [2020-06-11 13:26:25] calculate_statistics
[STOP] [2020-06-11 13:26:25] calculate_statistics
[START] [2020-06-11 13:26:25] complete_harvest_instance
[START] [2020-06-11 13:26:25] overall_tsv_creation
[INFO] [2020-06-11 13:26:25] Processing group of 8 in 1 batches of 10000
[INFO] [2020-06-11 13:27:17] 12 Traits (unfiltered)...
[INFO] [2020-06-11 13:27:30] 12 Traits (filtered)...
[INFO] [2020-06-11 13:27:30] 0 Associations (filtered)...
[INFO] [2020-06-11 13:28:06] 54 metadata added.
[INFO] [2020-06-11 13:28:06] 0 metadata added.
[INFO] [2020-06-11 13:28:06] Average Time: 71.95
[INFO] [2020-06-11 13:28:06] Total Time: 1m41s
[STOP] [2020-06-11 13:28:06] overall_tsv_creation
[INFO] [2020-06-11 13:28:06] Done. Check your files:
[INFO] [2020-06-11 13:28:06] (8 lines) /app/public/data/kretschmar_bauma/publish_nodes.tsv
[INFO] [2020-06-11 13:28:06] (18 lines) /app/public/data/kretschmar_bauma/publish_node_ancestors.tsv
[INFO] [2020-06-11 13:28:06] (8 lines) /app/public/data/kretschmar_bauma/publish_scientific_names.tsv
[INFO] [2020-06-11 13:28:06] (13 lines) /app/public/data/kretschmar_bauma/publish_traits.tsv
[INFO] [2020-06-11 13:28:06] (55 lines) /app/public/data/kretschmar_bauma/publish_metadata.tsv
[STOP] [2020-06-11 13:28:06] complete_harvest_instance
[START] [2020-06-11 13:28:06] completed
[STOP] [2020-06-11 13:28:06] completed
[STOP] [2020-06-11 13:28:06] logged process, took 111.96

Latest Process

11 Jun 13:26 EXITED currently processing 0