Stage:
completed
Fetched:
30 Jul 14:30
Validated:
30 Jul 14:30
Deltas Created
30 Jul 14:30
Units Normalized:
30 Jul 14:30
Ancestry Built:
30 Jul 14:30
Nodes Matched:
30 Jul 14:30
Names Parsed:
30 Jul 14:30
New Models Stored:
30 Jul 14:30
Indexed:
30 Jul 14:30
Completed:
30 Jul 14:31
Time to Harvest:
less than a minute
Harvesting Log
(257 lines)
# Logfile created on 2020-07-30 12:48:41 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 12:48:41] logged process
[START] [2020-07-30 12:48:41] Creating resource from OpenData
[START] [2020-07-30 12:48:41] logged process
[START] [2020-07-30 12:48:41] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:48:42] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:48:42] Creating resource from OpenData
[INFO] [2020-07-30 12:48:59] ## HARVEST: type = -harvest
[START] [2020-07-30 12:49:08] logged process
[START] [2020-07-30 12:49:08] create_harvest_instance
[STOP] [2020-07-30 12:49:10] create_harvest_instance
[START] [2020-07-30 12:49:10] fetch_files
[STOP] [2020-07-30 12:49:10] fetch_files
[START] [2020-07-30 12:49:10] validate_each_file
[STOP] [2020-07-30 12:49:10] validate_each_file
[START] [2020-07-30 12:49:10] convert_to_csv
[CMD] [2020-07-30 12:49:10] /usr/bin/sort /app/public/converted_csv/burr_robinson_bu_refs_22260.csv > /app/public/converted_csv/burr_robinson_bu_refs_22260.csv_sorted
[CMD] [2020-07-30 12:49:10] /usr/bin/sort /app/public/converted_csv/burr_robinson_bu_nodes_22261.csv > /app/public/converted_csv/burr_robinson_bu_nodes_22261.csv_sorted
[CMD] [2020-07-30 12:49:10] /usr/bin/sort /app/public/converted_csv/burr_robinson_bu_occurrences_22262.csv > /app/public/converted_csv/burr_robinson_bu_occurrences_22262.csv_sorted
[CMD] [2020-07-30 12:49:10] /usr/bin/sort /app/public/converted_csv/burr_robinson_bu_measurements_22263.csv > /app/public/converted_csv/burr_robinson_bu_measurements_22263.csv_sorted
[STOP] [2020-07-30 12:49:10] convert_to_csv
[START] [2020-07-30 12:49:10] calculate_delta
[CMD] [2020-07-30 12:49:10] echo "0a" > /app/public/diff/burr_robinson_bu_refs_22260.diff
[CMD] [2020-07-30 12:49:10] tail -n +1 /app/public/converted_csv/burr_robinson_bu_refs_22260.csv >> /app/public/diff/burr_robinson_bu_refs_22260.diff
[CMD] [2020-07-30 12:49:10] echo "." >> /app/public/diff/burr_robinson_bu_refs_22260.diff
[CMD] [2020-07-30 12:49:10] echo "0a" > /app/public/diff/burr_robinson_bu_nodes_22261.diff
[CMD] [2020-07-30 12:49:10] tail -n +1 /app/public/converted_csv/burr_robinson_bu_nodes_22261.csv >> /app/public/diff/burr_robinson_bu_nodes_22261.diff
[CMD] [2020-07-30 12:49:10] echo "." >> /app/public/diff/burr_robinson_bu_nodes_22261.diff
[CMD] [2020-07-30 12:49:10] echo "0a" > /app/public/diff/burr_robinson_bu_occurrences_22262.diff
[CMD] [2020-07-30 12:49:10] tail -n +1 /app/public/converted_csv/burr_robinson_bu_occurrences_22262.csv >> /app/public/diff/burr_robinson_bu_occurrences_22262.diff
[CMD] [2020-07-30 12:49:10] echo "." >> /app/public/diff/burr_robinson_bu_occurrences_22262.diff
[CMD] [2020-07-30 12:49:10] echo "0a" > /app/public/diff/burr_robinson_bu_measurements_22263.diff
[CMD] [2020-07-30 12:49:10] tail -n +1 /app/public/converted_csv/burr_robinson_bu_measurements_22263.csv >> /app/public/diff/burr_robinson_bu_measurements_22263.diff
[CMD] [2020-07-30 12:49:10] echo "." >> /app/public/diff/burr_robinson_bu_measurements_22263.diff
[STOP] [2020-07-30 12:49:10] calculate_delta
[START] [2020-07-30 12:49:10] parse_diff_and_store
[INFO] [2020-07-30 12:49:10] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 12:49:10] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 12:49:10] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 12:49:10] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 12:49:10] Storing 1 ScientificNames
[INFO] [2020-07-30 12:49:10] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 12:49:10] Average Time: 0.0
[INFO] [2020-07-30 12:49:10] Total Time: 1s
[INFO] [2020-07-30 12:49:10] Storing 1 Nodes
[INFO] [2020-07-30 12:49:10] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 12:49:10] Average Time: 0.0
[INFO] [2020-07-30 12:49:10] Total Time: 1s
[INFO] [2020-07-30 12:49:10] Storing 1 Occurrences
[INFO] [2020-07-30 12:49:10] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 12:49:10] Average Time: 0.0
[INFO] [2020-07-30 12:49:10] Total Time: 1s
[INFO] [2020-07-30 12:49:10] Storing 3 Traits
[INFO] [2020-07-30 12:49:10] Processing group of 3 in 1 groups of 1000
[INFO] [2020-07-30 12:49:10] Average Time: 0.0
[INFO] [2020-07-30 12:49:10] Total Time: 1s
[INFO] [2020-07-30 12:49:10] Storing 2 MetaTraits
[INFO] [2020-07-30 12:49:10] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 12:49:10] Average Time: 0.0
[INFO] [2020-07-30 12:49:10] Total Time: 1s
[STOP] [2020-07-30 12:49:10] parse_diff_and_store
[START] [2020-07-30 12:49:10] resolve_keys
[STOP] [2020-07-30 12:49:15] resolve_keys
[ERR] [2020-07-30 12:49:15] ActiveRecord::StatementInvalid
[ERR] [2020-07-30 12:49:15] Lockfile::StolenLockError: Lockfile::StolenLockError: SELECT COUNT(*) FROM `articles_sections` WHERE (1=1) AND `articles_sections`.`harvest_id` = 3013
[ERR] [2020-07-30 12:49:15] ./config/initializers/core_extensions.rb:17:in `propagate_id'
[ERR] [2020-07-30 12:49:15] ../models/resource_harvester.rb:576:in `propagate_id'
[ERR] [2020-07-30 12:49:15] ../models/resource_harvester.rb:470:in `resolve_article_keys'
[ERR] [2020-07-30 12:49:15] ../models/resource_harvester.rb:428:in `resolve_keys'
[ERR] [2020-07-30 12:49:15] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2020-07-30 12:49:15] ../models/logged_process.rb:19:in `run_step'
[ERR] [2020-07-30 12:49:15] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2020-07-30 12:49:15] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2020-07-30 12:49:15] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2020-07-30 12:49:15] ../models/resource.rb:151:in `lock'
[ERR] [2020-07-30 12:49:15] ../models/resource_harvester.rb:72:in `start'
[ERR] [2020-07-30 12:49:15] ../models/resource.rb:232:in `harvest'
[ERR] [2020-07-30 12:49:15] bin/rails:4:in `require'
[ERR] [2020-07-30 12:49:15] bin/rails:4:in `<main>'
[STOP] [2020-07-30 12:49:15] logged process, took 7.23
[INFO] [2020-07-30 14:28:18] ## HARVEST: type = resume_-harvest
[START] [2020-07-30 14:28:41] logged process
[ERR] [2020-07-30 14:28:41][hdls] *****
[ERR] [2020-07-30 14:28:41][hdls] ***** HARVEST ATTEMPT FAILED: This resource is locked; assuming it is already running. Remove lock if not.
[ERR] [2020-07-30 14:28:41][hdls] *****
[INFO] [2020-07-30 14:30:09] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-07-30 14:30:12] ## remove_type: ScientificName
[INFO] [2020-07-30 14:30:12] ++ Calling delete_all on 1 instances...
[INFO] [2020-07-30 14:30:12] [14:30:12.229] Removed 1 Scientificnames
[INFO] [2020-07-30 14:30:12] ## remove_type: Vernacular
[INFO] [2020-07-30 14:30:12] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:30:12] [14:30:12.232] Removed 0 Vernaculars
[INFO] [2020-07-30 14:30:12] ## remove_type: Article
[INFO] [2020-07-30 14:30:12] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:30:12] [14:30:12.235] Removed 0 Articles
[INFO] [2020-07-30 14:30:12] ## remove_type: Medium
[INFO] [2020-07-30 14:30:12] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:30:12] [14:30:12.239] Removed 0 Media
[INFO] [2020-07-30 14:30:12] ## remove_type: Trait
[INFO] [2020-07-30 14:30:12] ++ Calling delete_all on 3 instances...
[INFO] [2020-07-30 14:30:12] [14:30:12.242] Removed 3 Traits
[INFO] [2020-07-30 14:30:12] ## remove_type: MetaTrait
[INFO] [2020-07-30 14:30:12] ++ Calling delete_all on 2 instances...
[INFO] [2020-07-30 14:30:12] [14:30:12.245] Removed 2 Metatraits
[INFO] [2020-07-30 14:30:12] ## remove_type: OccurrenceMetadatum
[INFO] [2020-07-30 14:30:12] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:30:12] [14:30:12.248] Removed 0 Occurrencemetadata
[INFO] [2020-07-30 14:30:12] ## remove_type: Assoc
[INFO] [2020-07-30 14:30:12] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:30:12] [14:30:12.250] Removed 0 Assocs
[INFO] [2020-07-30 14:30:12] ## remove_type: MetaAssoc
[INFO] [2020-07-30 14:30:12] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:30:12] [14:30:12.253] Removed 0 Metaassocs
[INFO] [2020-07-30 14:30:12] ## remove_type: Identifier
[INFO] [2020-07-30 14:30:12] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:30:12] [14:30:12.255] Removed 0 Identifiers
[INFO] [2020-07-30 14:30:12] ## remove_type: Reference
[INFO] [2020-07-30 14:30:12] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-30 14:30:12] [14:30:12.258] Removed 0 References
[INFO] [2020-07-30 14:30:12] ## remove_type: Node
[INFO] [2020-07-30 14:30:12] ++ Calling delete_all on 1 instances...
[INFO] [2020-07-30 14:30:12] [14:30:12.290] Removed 1 Nodes
[START] [2020-07-30 14:30:12] logged process
[START] [2020-07-30 14:30:12] Creating resource from OpenData
[START] [2020-07-30 14:30:12] logged process
[START] [2020-07-30 14:30:12] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:30:12] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:30:12] Creating resource from OpenData
[START] [2020-07-30 14:30:12] logged process
[START] [2020-07-30 14:30:12] create_harvest_instance
[STOP] [2020-07-30 14:30:14] create_harvest_instance
[START] [2020-07-30 14:30:14] fetch_files
[STOP] [2020-07-30 14:30:14] fetch_files
[START] [2020-07-30 14:30:14] validate_each_file
[STOP] [2020-07-30 14:30:14] validate_each_file
[START] [2020-07-30 14:30:14] convert_to_csv
[CMD] [2020-07-30 14:30:14] /usr/bin/sort /app/public/converted_csv/burr_robinson_bu_refs_22284.csv > /app/public/converted_csv/burr_robinson_bu_refs_22284.csv_sorted
[CMD] [2020-07-30 14:30:14] /usr/bin/sort /app/public/converted_csv/burr_robinson_bu_nodes_22285.csv > /app/public/converted_csv/burr_robinson_bu_nodes_22285.csv_sorted
[CMD] [2020-07-30 14:30:14] /usr/bin/sort /app/public/converted_csv/burr_robinson_bu_occurrences_22286.csv > /app/public/converted_csv/burr_robinson_bu_occurrences_22286.csv_sorted
[CMD] [2020-07-30 14:30:14] /usr/bin/sort /app/public/converted_csv/burr_robinson_bu_measurements_22287.csv > /app/public/converted_csv/burr_robinson_bu_measurements_22287.csv_sorted
[STOP] [2020-07-30 14:30:14] convert_to_csv
[START] [2020-07-30 14:30:14] calculate_delta
[CMD] [2020-07-30 14:30:14] echo "0a" > /app/public/diff/burr_robinson_bu_refs_22284.diff
[CMD] [2020-07-30 14:30:14] tail -n +1 /app/public/converted_csv/burr_robinson_bu_refs_22284.csv >> /app/public/diff/burr_robinson_bu_refs_22284.diff
[CMD] [2020-07-30 14:30:14] echo "." >> /app/public/diff/burr_robinson_bu_refs_22284.diff
[CMD] [2020-07-30 14:30:14] echo "0a" > /app/public/diff/burr_robinson_bu_nodes_22285.diff
[CMD] [2020-07-30 14:30:14] tail -n +1 /app/public/converted_csv/burr_robinson_bu_nodes_22285.csv >> /app/public/diff/burr_robinson_bu_nodes_22285.diff
[CMD] [2020-07-30 14:30:14] echo "." >> /app/public/diff/burr_robinson_bu_nodes_22285.diff
[CMD] [2020-07-30 14:30:14] echo "0a" > /app/public/diff/burr_robinson_bu_occurrences_22286.diff
[CMD] [2020-07-30 14:30:14] tail -n +1 /app/public/converted_csv/burr_robinson_bu_occurrences_22286.csv >> /app/public/diff/burr_robinson_bu_occurrences_22286.diff
[CMD] [2020-07-30 14:30:14] echo "." >> /app/public/diff/burr_robinson_bu_occurrences_22286.diff
[CMD] [2020-07-30 14:30:14] echo "0a" > /app/public/diff/burr_robinson_bu_measurements_22287.diff
[CMD] [2020-07-30 14:30:14] tail -n +1 /app/public/converted_csv/burr_robinson_bu_measurements_22287.csv >> /app/public/diff/burr_robinson_bu_measurements_22287.diff
[CMD] [2020-07-30 14:30:14] echo "." >> /app/public/diff/burr_robinson_bu_measurements_22287.diff
[STOP] [2020-07-30 14:30:14] calculate_delta
[START] [2020-07-30 14:30:14] parse_diff_and_store
[INFO] [2020-07-30 14:30:14] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 14:30:14] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 14:30:14] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 14:30:14] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 14:30:14] Storing 1 ScientificNames
[INFO] [2020-07-30 14:30:14] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 14:30:14] Average Time: 0.0
[INFO] [2020-07-30 14:30:14] Total Time: 1s
[INFO] [2020-07-30 14:30:14] Storing 1 Nodes
[INFO] [2020-07-30 14:30:14] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 14:30:14] Average Time: 0.0
[INFO] [2020-07-30 14:30:14] Total Time: 1s
[INFO] [2020-07-30 14:30:14] Storing 1 Occurrences
[INFO] [2020-07-30 14:30:14] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 14:30:14] Average Time: 0.0
[INFO] [2020-07-30 14:30:14] Total Time: 1s
[INFO] [2020-07-30 14:30:14] Storing 3 Traits
[INFO] [2020-07-30 14:30:14] Processing group of 3 in 1 groups of 1000
[INFO] [2020-07-30 14:30:14] Average Time: 0.0
[INFO] [2020-07-30 14:30:14] Total Time: 1s
[INFO] [2020-07-30 14:30:14] Storing 2 MetaTraits
[INFO] [2020-07-30 14:30:14] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 14:30:14] Average Time: 0.0
[INFO] [2020-07-30 14:30:14] Total Time: 1s
[STOP] [2020-07-30 14:30:14] parse_diff_and_store
[START] [2020-07-30 14:30:14] resolve_keys
[INFO] [2020-07-30 14:30:21] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 14:30:21] traits to occurrences...
[INFO] [2020-07-30 14:30:21] traits to nodes (through occurrences)...
[INFO] [2020-07-30 14:30:21] Traits to sex term...
[INFO] [2020-07-30 14:30:21] Traits to lifestage term...
[INFO] [2020-07-30 14:30:21] MetaTraits to traits...
[INFO] [2020-07-30 14:30:21] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 14:30:21] Assocs to occurrences...
[INFO] [2020-07-30 14:30:21] Assocs to nodes...
[INFO] [2020-07-30 14:30:21] Assoc to sex term...
[INFO] [2020-07-30 14:30:21] Assoc to lifestage term...
[STOP] [2020-07-30 14:30:21] resolve_keys
[START] [2020-07-30 14:30:21] hold_for_later_1
[STOP] [2020-07-30 14:30:21] hold_for_later_1
[START] [2020-07-30 14:30:21] hold_for_later_2
[STOP] [2020-07-30 14:30:21] hold_for_later_2
[START] [2020-07-30 14:30:21] resolve_missing_parents
[STOP] [2020-07-30 14:30:21] resolve_missing_parents
[START] [2020-07-30 14:30:21] rebuild_nodes
[START] [2020-07-30 14:30:21] Flattener#flatten
[START] [2020-07-30 14:30:21] Flattener#study_resource
[START] [2020-07-30 14:30:21] Flattener#build_ancestry
[STOP] [2020-07-30 14:30:21] Flattener#build_ancestry
[INFO] [2020-07-30 14:30:21] 1 ancestry keys
[START] [2020-07-30 14:30:21] build_node_ancestors
[INFO] [2020-07-30 14:30:21] old ancestors deleted.
[STOP] [2020-07-30 14:30:21] build_node_ancestors
[WARN] [2020-07-30 14:30:21] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 14:30:21] Flattener#flatten
[STOP] [2020-07-30 14:30:21] rebuild_nodes
[START] [2020-07-30 14:30:21] resolve_missing_media_owners
[STOP] [2020-07-30 14:30:21] resolve_missing_media_owners
[START] [2020-07-30 14:30:21] sanitize_media_verbatims
[STOP] [2020-07-30 14:30:21] sanitize_media_verbatims
[START] [2020-07-30 14:30:21] queue_downloads
[STOP] [2020-07-30 14:30:21] queue_downloads
[START] [2020-07-30 14:30:21] parse_names
[WARN] [2020-07-30 14:30:21] I see 1 names which still need to be parsed.
[STOP] [2020-07-30 14:30:23] parse_names
[START] [2020-07-30 14:30:23] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 14:30:23] denormalize_canonical_names_to_nodes
[START] [2020-07-30 14:30:23] match_nodes
[START] [2020-07-30 14:30:23] map_all_nodes_to_pages
[STOP] [2020-07-30 14:30:23] map_all_nodes_to_pages
[INFO] [2020-07-30 14:30:23] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-07-30 14:30:23] update_nodes
[STOP] [2020-07-30 14:30:23] update_nodes
[STOP] [2020-07-30 14:30:23] match_nodes
[START] [2020-07-30 14:30:23] reindex_search
[STOP] [2020-07-30 14:30:23] reindex_search
[START] [2020-07-30 14:30:23] normalize_units
[STOP] [2020-07-30 14:30:23] normalize_units
[START] [2020-07-30 14:30:23] calculate_statistics
[2020-07-30 14:30:23] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 14:30:23] calculate_statistics
[START] [2020-07-30 14:30:23] complete_harvest_instance
[START] [2020-07-30 14:30:23] overall_tsv_creation
[INFO] [2020-07-30 14:30:23] Processing group of 1 in 1 batches of 10000
[INFO] [2020-07-30 14:31:11] 1 Traits (unfiltered)...
[INFO] [2020-07-30 14:31:45] 1 Traits (filtered)...
[INFO] [2020-07-30 14:31:45] 0 Associations (filtered)...
[INFO] [2020-07-30 14:31:45] 4 metadata added.
[INFO] [2020-07-30 14:31:45] 0 metadata added.
[INFO] [2020-07-30 14:31:45] Average Time: 55.47
[INFO] [2020-07-30 14:31:45] Total Time: 1m23s
[STOP] [2020-07-30 14:31:45] overall_tsv_creation
[INFO] [2020-07-30 14:31:45] Done. Check your files:
[INFO] [2020-07-30 14:31:45] (1 lines) /app/public/data/burr_robinson_bu/publish_nodes.tsv
[INFO] [2020-07-30 14:31:45] (1 lines) /app/public/data/burr_robinson_bu/publish_scientific_names.tsv
[INFO] [2020-07-30 14:31:45] (2 lines) /app/public/data/burr_robinson_bu/publish_traits.tsv
[INFO] [2020-07-30 14:31:45] (3 lines) /app/public/data/burr_robinson_bu/publish_metadata.tsv
[STOP] [2020-07-30 14:31:45] complete_harvest_instance
[START] [2020-07-30 14:31:45] completed
[STOP] [2020-07-30 14:31:45] completed
[STOP] [2020-07-30 14:31:45] logged process, took 92.71
Latest Process