Harvest for Yen 2012 Created 30 Jul 15:12

Stage: completed
Fetched: 30 Jul 15:12
Validated: 30 Jul 15:12
Deltas Created 30 Jul 15:12
Units Normalized: 30 Jul 15:12
Ancestry Built: 30 Jul 15:12
Nodes Matched: 30 Jul 15:12
Names Parsed: 30 Jul 15:12
New Models Stored: 30 Jul 15:12
Indexed: 30 Jul 15:12
Completed: 30 Jul 15:13
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2020-07-30 15:08:45 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 15:08:45] logged process
[START] [2020-07-30 15:08:45] Creating resource from OpenData
[START] [2020-07-30 15:08:45] logged process
[START] [2020-07-30 15:08:45] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 15:08:45] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 15:08:45] Creating resource from OpenData
[INFO] [2020-07-30 15:08:58] ## HARVEST: type = -harvest
[START] [2020-07-30 15:09:21] logged process
[START] [2020-07-30 15:09:21] create_harvest_instance
[STOP] [2020-07-30 15:09:22] create_harvest_instance
[START] [2020-07-30 15:09:22] fetch_files
[STOP] [2020-07-30 15:09:22] fetch_files
[START] [2020-07-30 15:09:22] validate_each_file
[STOP] [2020-07-30 15:09:22] validate_each_file
[START] [2020-07-30 15:09:22] convert_to_csv
[CMD] [2020-07-30 15:09:22] /usr/bin/sort /app/public/converted_csv/yen_yen_2012_refs_22376.csv > /app/public/converted_csv/yen_yen_2012_refs_22376.csv_sorted
[CMD] [2020-07-30 15:09:22] /usr/bin/sort /app/public/converted_csv/yen_yen_2012_nodes_22377.csv > /app/public/converted_csv/yen_yen_2012_nodes_22377.csv_sorted
[CMD] [2020-07-30 15:09:22] /usr/bin/sort /app/public/converted_csv/yen_yen_2012_occurrences_22378.csv > /app/public/converted_csv/yen_yen_2012_occurrences_22378.csv_sorted
[CMD] [2020-07-30 15:09:22] /usr/bin/sort /app/public/converted_csv/yen_yen_2012_measurements_22379.csv > /app/public/converted_csv/yen_yen_2012_measurements_22379.csv_sorted
[STOP] [2020-07-30 15:09:22] convert_to_csv
[START] [2020-07-30 15:09:22] calculate_delta
[CMD] [2020-07-30 15:09:22] echo "0a" > /app/public/diff/yen_yen_2012_refs_22376.diff
[CMD] [2020-07-30 15:09:22] tail -n +1 /app/public/converted_csv/yen_yen_2012_refs_22376.csv >> /app/public/diff/yen_yen_2012_refs_22376.diff
[CMD] [2020-07-30 15:09:22] echo "." >> /app/public/diff/yen_yen_2012_refs_22376.diff
[CMD] [2020-07-30 15:09:22] echo "0a" > /app/public/diff/yen_yen_2012_nodes_22377.diff
[CMD] [2020-07-30 15:09:22] tail -n +1 /app/public/converted_csv/yen_yen_2012_nodes_22377.csv >> /app/public/diff/yen_yen_2012_nodes_22377.diff
[CMD] [2020-07-30 15:09:22] echo "." >> /app/public/diff/yen_yen_2012_nodes_22377.diff
[CMD] [2020-07-30 15:09:22] echo "0a" > /app/public/diff/yen_yen_2012_occurrences_22378.diff
[CMD] [2020-07-30 15:09:22] tail -n +1 /app/public/converted_csv/yen_yen_2012_occurrences_22378.csv >> /app/public/diff/yen_yen_2012_occurrences_22378.diff
[CMD] [2020-07-30 15:09:22] echo "." >> /app/public/diff/yen_yen_2012_occurrences_22378.diff
[CMD] [2020-07-30 15:09:22] echo "0a" > /app/public/diff/yen_yen_2012_measurements_22379.diff
[CMD] [2020-07-30 15:09:22] tail -n +1 /app/public/converted_csv/yen_yen_2012_measurements_22379.csv >> /app/public/diff/yen_yen_2012_measurements_22379.diff
[CMD] [2020-07-30 15:09:22] echo "." >> /app/public/diff/yen_yen_2012_measurements_22379.diff
[STOP] [2020-07-30 15:09:22] calculate_delta
[START] [2020-07-30 15:09:22] parse_diff_and_store
[INFO] [2020-07-30 15:09:22] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 15:09:22] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 15:09:22] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 15:09:22] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 15:09:22] Storing 1 ScientificNames
[INFO] [2020-07-30 15:09:22] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 15:09:22] Average Time: 0.0
[INFO] [2020-07-30 15:09:22] Total Time: 1s
[INFO] [2020-07-30 15:09:22] Storing 1 Nodes
[INFO] [2020-07-30 15:09:22] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 15:09:22] Average Time: 0.0
[INFO] [2020-07-30 15:09:22] Total Time: 1s
[INFO] [2020-07-30 15:09:22] Storing 1 Occurrences
[INFO] [2020-07-30 15:09:22] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 15:09:22] Average Time: NaN
[INFO] [2020-07-30 15:09:22] Total Time: 1s
[STOP] [2020-07-30 15:09:22] parse_diff_and_store
[ERR] [2020-07-30 15:09:22] ActiveRecord::NotNullViolation
[ERR] [2020-07-30 15:09:22] Mysql2::Error: Column 'resource_pk' cannot be null: INSERT INTO `occurrences` (`id`,`harvest_id`,`resource_pk`,`node_id`,`node_resource_pk`,`sex_term_id`,`lifestage_term_id`,`resource_id`) VALUES (NULL,3027,NULL,NULL,'Copepoda',NULL,NULL,988)
[ERR] [2020-07-30 15:09:22] ../models/resource_harvester.rb:395:in `block (3 levels) in store_new'
[ERR] [2020-07-30 15:09:22] ../models/resource_harvester.rb:394:in `each'
[ERR] [2020-07-30 15:09:22] ../models/resource_harvester.rb:394:in `rescue in block (2 levels) in store_new'
[ERR] [2020-07-30 15:09:22] ../models/resource_harvester.rb:383:in `block (2 levels) in store_new'
[ERR] [2020-07-30 15:09:22] ../models/logged_process.rb:34:in `block in in_groups'
[ERR] [2020-07-30 15:09:22] ../models/logged_process.rb:32:in `in_groups'
[ERR] [2020-07-30 15:09:22] ../models/resource_harvester.rb:379:in `block in store_new'
[ERR] [2020-07-30 15:09:22] ../models/resource_harvester.rb:373:in `each'
[ERR] [2020-07-30 15:09:22] ../models/resource_harvester.rb:373:in `store_new'
[ERR] [2020-07-30 15:09:22] ../models/resource_harvester.rb:347:in `parse_diff_and_store'
[ERR] [2020-07-30 15:09:22] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2020-07-30 15:09:22] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-07-30 15:09:22] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2020-07-30 15:09:22] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2020-07-30 15:09:22] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2020-07-30 15:09:22] ../models/resource.rb:151:in `lock'
[ERR] [2020-07-30 15:09:22] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-07-30 15:09:22] ../models/resource.rb:232:in `harvest'
[ERR] [2020-07-30 15:09:22] bin/rails:4:in `require'
[ERR] [2020-07-30 15:09:22] bin/rails:4:in `<main>'
[STOP] [2020-07-30 15:09:22] logged process, took 1.72
[INFO] [2020-07-30 15:12:07] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-07-30 15:12:10] ## remove_type: ScientificName
[INFO] [2020-07-30 15:12:10] ++ Calling delete_all on 1 instances...
[INFO] [2020-07-30 15:12:10] [15:12:10.596] Removed 1 Scientificnames
[INFO] [2020-07-30 15:12:10] ## remove_type: Vernacular
[INFO] [2020-07-30 15:12:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 15:12:10] [15:12:10.598] Removed 0 Vernaculars
[INFO] [2020-07-30 15:12:10] ## remove_type: Article
[INFO] [2020-07-30 15:12:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 15:12:10] [15:12:10.602] Removed 0 Articles
[INFO] [2020-07-30 15:12:10] ## remove_type: Medium
[INFO] [2020-07-30 15:12:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 15:12:10] [15:12:10.605] Removed 0 Media
[INFO] [2020-07-30 15:12:10] ## remove_type: Trait
[INFO] [2020-07-30 15:12:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 15:12:10] [15:12:10.608] Removed 0 Traits
[INFO] [2020-07-30 15:12:10] ## remove_type: MetaTrait
[INFO] [2020-07-30 15:12:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 15:12:10] [15:12:10.611] Removed 0 Metatraits
[INFO] [2020-07-30 15:12:10] ## remove_type: OccurrenceMetadatum
[INFO] [2020-07-30 15:12:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 15:12:10] [15:12:10.614] Removed 0 Occurrencemetadata
[INFO] [2020-07-30 15:12:10] ## remove_type: Assoc
[INFO] [2020-07-30 15:12:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 15:12:10] [15:12:10.617] Removed 0 Assocs
[INFO] [2020-07-30 15:12:10] ## remove_type: MetaAssoc
[INFO] [2020-07-30 15:12:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 15:12:10] [15:12:10.620] Removed 0 Metaassocs
[INFO] [2020-07-30 15:12:10] ## remove_type: Identifier
[INFO] [2020-07-30 15:12:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 15:12:10] [15:12:10.622] Removed 0 Identifiers
[INFO] [2020-07-30 15:12:10] ## remove_type: Reference
[INFO] [2020-07-30 15:12:10] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 15:12:10] [15:12:10.625] Removed 0 References
[INFO] [2020-07-30 15:12:10] ## remove_type: Node
[INFO] [2020-07-30 15:12:10] ++ Calling delete_all on 1 instances...
[INFO] [2020-07-30 15:12:10] [15:12:10.658] Removed 1 Nodes
[START] [2020-07-30 15:12:11] logged process
[START] [2020-07-30 15:12:11] Creating resource from OpenData
[START] [2020-07-30 15:12:11] logged process
[START] [2020-07-30 15:12:11] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 15:12:11] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 15:12:11] Creating resource from OpenData
[START] [2020-07-30 15:12:11] logged process
[START] [2020-07-30 15:12:11] create_harvest_instance
[STOP] [2020-07-30 15:12:12] create_harvest_instance
[START] [2020-07-30 15:12:12] fetch_files
[STOP] [2020-07-30 15:12:12] fetch_files
[START] [2020-07-30 15:12:12] validate_each_file
[STOP] [2020-07-30 15:12:12] validate_each_file
[START] [2020-07-30 15:12:12] convert_to_csv
[CMD] [2020-07-30 15:12:12] /usr/bin/sort /app/public/converted_csv/yen_yen_2012_refs_22388.csv > /app/public/converted_csv/yen_yen_2012_refs_22388.csv_sorted
[CMD] [2020-07-30 15:12:12] /usr/bin/sort /app/public/converted_csv/yen_yen_2012_nodes_22389.csv > /app/public/converted_csv/yen_yen_2012_nodes_22389.csv_sorted
[CMD] [2020-07-30 15:12:12] /usr/bin/sort /app/public/converted_csv/yen_yen_2012_occurrences_22390.csv > /app/public/converted_csv/yen_yen_2012_occurrences_22390.csv_sorted
[CMD] [2020-07-30 15:12:12] /usr/bin/sort /app/public/converted_csv/yen_yen_2012_measurements_22391.csv > /app/public/converted_csv/yen_yen_2012_measurements_22391.csv_sorted
[STOP] [2020-07-30 15:12:12] convert_to_csv
[START] [2020-07-30 15:12:12] calculate_delta
[CMD] [2020-07-30 15:12:12] echo "0a" > /app/public/diff/yen_yen_2012_refs_22388.diff
[CMD] [2020-07-30 15:12:12] tail -n +1 /app/public/converted_csv/yen_yen_2012_refs_22388.csv >> /app/public/diff/yen_yen_2012_refs_22388.diff
[CMD] [2020-07-30 15:12:12] echo "." >> /app/public/diff/yen_yen_2012_refs_22388.diff
[CMD] [2020-07-30 15:12:12] echo "0a" > /app/public/diff/yen_yen_2012_nodes_22389.diff
[CMD] [2020-07-30 15:12:12] tail -n +1 /app/public/converted_csv/yen_yen_2012_nodes_22389.csv >> /app/public/diff/yen_yen_2012_nodes_22389.diff
[CMD] [2020-07-30 15:12:12] echo "." >> /app/public/diff/yen_yen_2012_nodes_22389.diff
[CMD] [2020-07-30 15:12:12] echo "0a" > /app/public/diff/yen_yen_2012_occurrences_22390.diff
[CMD] [2020-07-30 15:12:12] tail -n +1 /app/public/converted_csv/yen_yen_2012_occurrences_22390.csv >> /app/public/diff/yen_yen_2012_occurrences_22390.diff
[CMD] [2020-07-30 15:12:12] echo "." >> /app/public/diff/yen_yen_2012_occurrences_22390.diff
[CMD] [2020-07-30 15:12:12] echo "0a" > /app/public/diff/yen_yen_2012_measurements_22391.diff
[CMD] [2020-07-30 15:12:12] tail -n +1 /app/public/converted_csv/yen_yen_2012_measurements_22391.csv >> /app/public/diff/yen_yen_2012_measurements_22391.diff
[CMD] [2020-07-30 15:12:12] echo "." >> /app/public/diff/yen_yen_2012_measurements_22391.diff
[STOP] [2020-07-30 15:12:12] calculate_delta
[START] [2020-07-30 15:12:12] parse_diff_and_store
[INFO] [2020-07-30 15:12:12] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 15:12:12] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 15:12:12] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 15:12:12] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 15:12:12] Storing 1 ScientificNames
[INFO] [2020-07-30 15:12:12] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 15:12:13] Average Time: 0.0
[INFO] [2020-07-30 15:12:13] Total Time: 1s
[INFO] [2020-07-30 15:12:13] Storing 1 Nodes
[INFO] [2020-07-30 15:12:13] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 15:12:13] Average Time: 0.0
[INFO] [2020-07-30 15:12:13] Total Time: 1s
[INFO] [2020-07-30 15:12:13] Storing 1 Occurrences
[INFO] [2020-07-30 15:12:13] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 15:12:13] Average Time: 0.0
[INFO] [2020-07-30 15:12:13] Total Time: 1s
[INFO] [2020-07-30 15:12:13] Storing 3 Traits
[INFO] [2020-07-30 15:12:13] Processing group of 3 in 1 groups of 1000
[INFO] [2020-07-30 15:12:13] Average Time: 0.0
[INFO] [2020-07-30 15:12:13] Total Time: 1s
[INFO] [2020-07-30 15:12:13] Storing 2 MetaTraits
[INFO] [2020-07-30 15:12:13] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 15:12:13] Average Time: 0.0
[INFO] [2020-07-30 15:12:13] Total Time: 1s
[STOP] [2020-07-30 15:12:13] parse_diff_and_store
[START] [2020-07-30 15:12:13] resolve_keys
[INFO] [2020-07-30 15:12:19] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 15:12:19] traits to occurrences...
[INFO] [2020-07-30 15:12:19] traits to nodes (through occurrences)...
[INFO] [2020-07-30 15:12:19] Traits to sex term...
[INFO] [2020-07-30 15:12:19] Traits to lifestage term...
[INFO] [2020-07-30 15:12:19] MetaTraits to traits...
[INFO] [2020-07-30 15:12:19] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 15:12:19] Assocs to occurrences...
[INFO] [2020-07-30 15:12:19] Assocs to nodes...
[INFO] [2020-07-30 15:12:19] Assoc to sex term...
[INFO] [2020-07-30 15:12:19] Assoc to lifestage term...
[STOP] [2020-07-30 15:12:19] resolve_keys
[START] [2020-07-30 15:12:19] hold_for_later_1
[STOP] [2020-07-30 15:12:19] hold_for_later_1
[START] [2020-07-30 15:12:19] hold_for_later_2
[STOP] [2020-07-30 15:12:19] hold_for_later_2
[START] [2020-07-30 15:12:19] resolve_missing_parents
[STOP] [2020-07-30 15:12:19] resolve_missing_parents
[START] [2020-07-30 15:12:19] rebuild_nodes
[START] [2020-07-30 15:12:19] Flattener#flatten
[START] [2020-07-30 15:12:19] Flattener#study_resource
[START] [2020-07-30 15:12:19] Flattener#build_ancestry
[STOP] [2020-07-30 15:12:19] Flattener#build_ancestry
[INFO] [2020-07-30 15:12:19] 1 ancestry keys
[START] [2020-07-30 15:12:19] build_node_ancestors
[INFO] [2020-07-30 15:12:19] old ancestors deleted.
[STOP] [2020-07-30 15:12:19] build_node_ancestors
[WARN] [2020-07-30 15:12:19] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 15:12:19] Flattener#flatten
[STOP] [2020-07-30 15:12:19] rebuild_nodes
[START] [2020-07-30 15:12:19] resolve_missing_media_owners
[STOP] [2020-07-30 15:12:19] resolve_missing_media_owners
[START] [2020-07-30 15:12:19] sanitize_media_verbatims
[STOP] [2020-07-30 15:12:19] sanitize_media_verbatims
[START] [2020-07-30 15:12:19] queue_downloads
[STOP] [2020-07-30 15:12:19] queue_downloads
[START] [2020-07-30 15:12:19] parse_names
[WARN] [2020-07-30 15:12:19] I see 1 names which still need to be parsed.
[STOP] [2020-07-30 15:12:20] parse_names
[START] [2020-07-30 15:12:20] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 15:12:20] denormalize_canonical_names_to_nodes
[START] [2020-07-30 15:12:20] match_nodes
[START] [2020-07-30 15:12:20] map_all_nodes_to_pages
[STOP] [2020-07-30 15:12:20] map_all_nodes_to_pages
[INFO] [2020-07-30 15:12:20] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-07-30 15:12:20] update_nodes
[STOP] [2020-07-30 15:12:20] update_nodes
[STOP] [2020-07-30 15:12:20] match_nodes
[START] [2020-07-30 15:12:20] reindex_search
[STOP] [2020-07-30 15:12:21] reindex_search
[START] [2020-07-30 15:12:21] normalize_units
[STOP] [2020-07-30 15:12:21] normalize_units
[START] [2020-07-30 15:12:21] calculate_statistics
[2020-07-30 15:12:21] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 15:12:21] calculate_statistics
[START] [2020-07-30 15:12:21] complete_harvest_instance
[START] [2020-07-30 15:12:21] overall_tsv_creation
[INFO] [2020-07-30 15:12:21] Processing group of 1 in 1 batches of 10000
[INFO] [2020-07-30 15:13:09] 1 Traits (unfiltered)...
[INFO] [2020-07-30 15:13:43] 1 Traits (filtered)...
[INFO] [2020-07-30 15:13:43] 0 Associations (filtered)...
[INFO] [2020-07-30 15:13:43] 4 metadata added.
[INFO] [2020-07-30 15:13:43] 0 metadata added.
[INFO] [2020-07-30 15:13:43] Average Time: 55.82
[INFO] [2020-07-30 15:13:43] Total Time: 1m23s
[STOP] [2020-07-30 15:13:43] overall_tsv_creation
[INFO] [2020-07-30 15:13:43] Done. Check your files:
[INFO] [2020-07-30 15:13:43] (1 lines) /app/public/data/yen_yen_2012/publish_nodes.tsv
[INFO] [2020-07-30 15:13:43] (1 lines) /app/public/data/yen_yen_2012/publish_scientific_names.tsv
[INFO] [2020-07-30 15:13:43] (2 lines) /app/public/data/yen_yen_2012/publish_traits.tsv
[INFO] [2020-07-30 15:13:43] (3 lines) /app/public/data/yen_yen_2012/publish_metadata.tsv
[STOP] [2020-07-30 15:13:43] complete_harvest_instance
[START] [2020-07-30 15:13:43] completed
[STOP] [2020-07-30 15:13:43] completed
[STOP] [2020-07-30 15:13:43] logged process, took 92.64

Latest Process