Harvest for Ankel Simons 2008 Created 06 Apr 17:52

Stage: completed
Fetched: 06 Apr 17:52
Validated: 06 Apr 17:52
Deltas Created 06 Apr 17:52
Units Normalized: 06 Apr 17:52
Ancestry Built: 06 Apr 17:52
Nodes Matched: 06 Apr 17:52
Names Parsed: 06 Apr 17:52
New Models Stored: 06 Apr 17:52
Indexed: 06 Apr 17:52
Completed: 06 Apr 17:54
Time to Harvest: less than a minute

Harvesting Log (most recent first)

# Logfile created on 2021-02-03 09:22:58 -0500 by logger.rb/v1.4.2
[START] [2021-02-03 09:22:58] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 09:22:58] Creating resource from OpenData
[START] [2021-02-03 09:22:58] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 09:22:58] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 09:22:58] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 09:22:58] Creating resource from OpenData
[INFO] [2021-02-03 09:25:13] ## HARVEST: type = -harvest
[START] [2021-02-03 09:25:15] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 09:25:15] create_harvest_instance
[STOP] [2021-02-03 09:25:16] create_harvest_instance
[START] [2021-02-03 09:25:16] fetch_files
[STOP] [2021-02-03 09:25:16] fetch_files
[START] [2021-02-03 09:25:16] validate_each_file
[STOP] [2021-02-03 09:25:16] validate_each_file
[START] [2021-02-03 09:25:16] convert_to_csv
[CMD] [2021-02-03 09:25:16] /usr/bin/sort /app/public/converted_csv/ankel_simons_ank_nodes_26437.csv > /app/public/converted_csv/ankel_simons_ank_nodes_26437.csv_sorted
[CMD] [2021-02-03 09:25:16] /usr/bin/sort /app/public/converted_csv/ankel_simons_ank_occurrences_26438.csv > /app/public/converted_csv/ankel_simons_ank_occurrences_26438.csv_sorted
[CMD] [2021-02-03 09:25:16] /usr/bin/sort /app/public/converted_csv/ankel_simons_ank_measurements_26439.csv > /app/public/converted_csv/ankel_simons_ank_measurements_26439.csv_sorted
[STOP] [2021-02-03 09:25:16] convert_to_csv
[START] [2021-02-03 09:25:16] calculate_delta
[CMD] [2021-02-03 09:25:16] echo "0a" > /app/public/diff/ankel_simons_ank_nodes_26437.diff
[CMD] [2021-02-03 09:25:16] tail -n +1 /app/public/converted_csv/ankel_simons_ank_nodes_26437.csv >> /app/public/diff/ankel_simons_ank_nodes_26437.diff
[CMD] [2021-02-03 09:25:16] echo "." >> /app/public/diff/ankel_simons_ank_nodes_26437.diff
[CMD] [2021-02-03 09:25:16] echo "0a" > /app/public/diff/ankel_simons_ank_occurrences_26438.diff
[CMD] [2021-02-03 09:25:16] tail -n +1 /app/public/converted_csv/ankel_simons_ank_occurrences_26438.csv >> /app/public/diff/ankel_simons_ank_occurrences_26438.diff
[CMD] [2021-02-03 09:25:16] echo "." >> /app/public/diff/ankel_simons_ank_occurrences_26438.diff
[CMD] [2021-02-03 09:25:16] echo "0a" > /app/public/diff/ankel_simons_ank_measurements_26439.diff
[CMD] [2021-02-03 09:25:16] tail -n +1 /app/public/converted_csv/ankel_simons_ank_measurements_26439.csv >> /app/public/diff/ankel_simons_ank_measurements_26439.diff
[CMD] [2021-02-03 09:25:16] echo "." >> /app/public/diff/ankel_simons_ank_measurements_26439.diff
[STOP] [2021-02-03 09:25:16] calculate_delta
[START] [2021-02-03 09:25:16] parse_diff_and_store
[INFO] [2021-02-03 09:25:16] Loading nodes diff file into memory (true lines)...
[INFO] [2021-02-03 09:25:16] Loading occurrences diff file into memory (true lines)...
[INFO] [2021-02-03 09:25:16] Loading measurements diff file into memory (true lines)...
[STOP] [2021-02-03 09:25:17] parse_diff_and_store
[ERR] [2021-02-03 09:25:17] RuntimeError
[ERR] [2021-02-03 09:25:17] Missing Term for URI `http://purl.obolibrary.org/obo/VT_0001504`, must be added!
[ERR] [2021-02-03 09:25:17] ../models/store/model_builder.rb:635:in `fail_on_bad_uri'
[ERR] [2021-02-03 09:25:17] ../models/store/model_builder.rb:408:in `build_trait'
[ERR] [2021-02-03 09:25:17] ../models/store/model_builder.rb:28:in `build_models'
[ERR] [2021-02-03 09:25:17] ../models/resource_harvester.rb:359:in `block (3 levels) in parse_diff_and_store'
[ERR] [2021-02-03 09:25:17] ../models/csv_parser.rb:111:in `block in diff_as_hashes'
[ERR] [2021-02-03 09:25:17] ../models/csv_parser.rb:28:in `block in line_at_a_time'
[ERR] [2021-02-03 09:25:17] ../models/csv_parser.rb:25:in `line_at_a_time'
[ERR] [2021-02-03 09:25:17] ../models/csv_parser.rb:96:in `diff_as_hashes'
[ERR] [2021-02-03 09:25:17] ../models/resource_harvester.rb:313:in `block (2 levels) in parse_diff_and_store'
[ERR] [2021-02-03 09:25:17] ../models/logged_process.rb:70:in `enter_group'
[ERR] [2021-02-03 09:25:17] ../models/resource_harvester.rb:312:in `block in parse_diff_and_store'
[ERR] [2021-02-03 09:25:17] ../models/resource_harvester.rb:702:in `block in each_diff'
[ERR] [2021-02-03 09:25:17] ../models/resource_harvester.rb:691:in `each_diff'
[ERR] [2021-02-03 09:25:17] ../models/resource_harvester.rb:307:in `parse_diff_and_store'
[ERR] [2021-02-03 09:25:17] ../models/resource_harvester.rb:85:in `block (3 levels) in start'
[ERR] [2021-02-03 09:25:17] ../models/logged_process.rb:27:in `run_step'
[ERR] [2021-02-03 09:25:17] ../models/resource_harvester.rb:85:in `block (2 levels) in start'
[ERR] [2021-02-03 09:25:17] ../models/resource_harvester.rb:74:in `each_key'
[ERR] [2021-02-03 09:25:17] ../models/resource_harvester.rb:74:in `block in start'
[ERR] [2021-02-03 09:25:17] ../models/resource.rb:159:in `lock'
[ERR] [2021-02-03 09:25:17] ../models/resource_harvester.rb:72:in `start'
[ERR] [2021-02-03 09:25:17] ../models/resource.rb:245:in `harvest'
[ERR] [2021-02-03 09:25:17] bin/rails:4:in `require'
[ERR] [2021-02-03 09:25:17] bin/rails:4:in `<main>'
[STOP] [2021-02-03 09:25:17] logged process, took 2.5
[INFO] [2021-02-03 09:31:36] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-02-03 09:31:38] ## remove_type: ScientificName
[INFO] [2021-02-03 09:31:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 09:31:38] [09:31:38.656] Removed 0 Scientificnames
[INFO] [2021-02-03 09:31:38] ## remove_type: Vernacular
[INFO] [2021-02-03 09:31:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 09:31:38] [09:31:38.658] Removed 0 Vernaculars
[INFO] [2021-02-03 09:31:38] ## remove_type: Article
[INFO] [2021-02-03 09:31:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 09:31:38] [09:31:38.661] Removed 0 Articles
[INFO] [2021-02-03 09:31:38] ## remove_type: Medium
[INFO] [2021-02-03 09:31:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 09:31:38] [09:31:38.665] Removed 0 Media
[INFO] [2021-02-03 09:31:38] ## remove_type: Trait
[INFO] [2021-02-03 09:31:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 09:31:38] [09:31:38.669] Removed 0 Traits
[INFO] [2021-02-03 09:31:38] ## remove_type: MetaTrait
[INFO] [2021-02-03 09:31:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 09:31:38] [09:31:38.672] Removed 0 Metatraits
[INFO] [2021-02-03 09:31:38] ## remove_type: OccurrenceMetadatum
[INFO] [2021-02-03 09:31:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 09:31:38] [09:31:38.674] Removed 0 Occurrencemetadata
[INFO] [2021-02-03 09:31:38] ## remove_type: Assoc
[INFO] [2021-02-03 09:31:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 09:31:38] [09:31:38.677] Removed 0 Assocs
[INFO] [2021-02-03 09:31:38] ## remove_type: MetaAssoc
[INFO] [2021-02-03 09:31:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 09:31:38] [09:31:38.679] Removed 0 Metaassocs
[INFO] [2021-02-03 09:31:38] ## remove_type: Identifier
[INFO] [2021-02-03 09:31:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 09:31:38] [09:31:38.682] Removed 0 Identifiers
[INFO] [2021-02-03 09:31:38] ## remove_type: Reference
[INFO] [2021-02-03 09:31:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 09:31:38] [09:31:38.685] Removed 0 References
[INFO] [2021-02-03 09:31:38] ## remove_type: Node
[INFO] [2021-02-03 09:31:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 09:31:38] [09:31:38.707] Removed 0 Nodes
[START] [2021-02-03 09:31:39] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 09:31:39] Creating resource from OpenData
[START] [2021-02-03 09:31:39] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 09:31:39] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 09:31:39] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 09:31:39] Creating resource from OpenData
[START] [2021-02-03 09:31:39] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 09:31:39] create_harvest_instance
[STOP] [2021-02-03 09:31:40] create_harvest_instance
[START] [2021-02-03 09:31:40] fetch_files
[STOP] [2021-02-03 09:31:40] fetch_files
[START] [2021-02-03 09:31:40] validate_each_file
[STOP] [2021-02-03 09:31:40] validate_each_file
[START] [2021-02-03 09:31:40] convert_to_csv
[CMD] [2021-02-03 09:31:40] /usr/bin/sort /app/public/converted_csv/ankel_simons_ank_nodes_26443.csv > /app/public/converted_csv/ankel_simons_ank_nodes_26443.csv_sorted
[CMD] [2021-02-03 09:31:40] /usr/bin/sort /app/public/converted_csv/ankel_simons_ank_occurrences_26444.csv > /app/public/converted_csv/ankel_simons_ank_occurrences_26444.csv_sorted
[CMD] [2021-02-03 09:31:40] /usr/bin/sort /app/public/converted_csv/ankel_simons_ank_measurements_26445.csv > /app/public/converted_csv/ankel_simons_ank_measurements_26445.csv_sorted
[STOP] [2021-02-03 09:31:40] convert_to_csv
[START] [2021-02-03 09:31:40] calculate_delta
[CMD] [2021-02-03 09:31:40] echo "0a" > /app/public/diff/ankel_simons_ank_nodes_26443.diff
[CMD] [2021-02-03 09:31:40] tail -n +1 /app/public/converted_csv/ankel_simons_ank_nodes_26443.csv >> /app/public/diff/ankel_simons_ank_nodes_26443.diff
[CMD] [2021-02-03 09:31:40] echo "." >> /app/public/diff/ankel_simons_ank_nodes_26443.diff
[CMD] [2021-02-03 09:31:40] echo "0a" > /app/public/diff/ankel_simons_ank_occurrences_26444.diff
[CMD] [2021-02-03 09:31:40] tail -n +1 /app/public/converted_csv/ankel_simons_ank_occurrences_26444.csv >> /app/public/diff/ankel_simons_ank_occurrences_26444.diff
[CMD] [2021-02-03 09:31:40] echo "." >> /app/public/diff/ankel_simons_ank_occurrences_26444.diff
[CMD] [2021-02-03 09:31:40] echo "0a" > /app/public/diff/ankel_simons_ank_measurements_26445.diff
[CMD] [2021-02-03 09:31:40] tail -n +1 /app/public/converted_csv/ankel_simons_ank_measurements_26445.csv >> /app/public/diff/ankel_simons_ank_measurements_26445.diff
[CMD] [2021-02-03 09:31:40] echo "." >> /app/public/diff/ankel_simons_ank_measurements_26445.diff
[STOP] [2021-02-03 09:31:40] calculate_delta
[START] [2021-02-03 09:31:40] parse_diff_and_store
[INFO] [2021-02-03 09:31:40] Loading nodes diff file into memory (true lines)...
[INFO] [2021-02-03 09:31:41] Loading occurrences diff file into memory (true lines)...
[INFO] [2021-02-03 09:31:41] Loading measurements diff file into memory (true lines)...
[INFO] [2021-02-03 09:31:41] Storing 17 ScientificNames
[INFO] [2021-02-03 09:31:41] Processing group of 17 in 1 groups of 1000
[INFO] [2021-02-03 09:31:41] Average Time: 0.01
[INFO] [2021-02-03 09:31:41] Total Time: 1s
[INFO] [2021-02-03 09:31:41] Storing 17 Nodes
[INFO] [2021-02-03 09:31:41] Processing group of 17 in 1 groups of 1000
[INFO] [2021-02-03 09:31:41] Average Time: 0.01
[INFO] [2021-02-03 09:31:41] Total Time: 1s
[INFO] [2021-02-03 09:31:41] Storing 17 Occurrences
[INFO] [2021-02-03 09:31:41] Processing group of 17 in 1 groups of 1000
[INFO] [2021-02-03 09:31:42] Average Time: 0.01
[INFO] [2021-02-03 09:31:42] Total Time: 1s
[INFO] [2021-02-03 09:31:42] Storing 34 Traits
[INFO] [2021-02-03 09:31:42] Processing group of 34 in 1 groups of 1000
[INFO] [2021-02-03 09:31:42] Average Time: 0.07
[INFO] [2021-02-03 09:31:42] Total Time: 1s
[INFO] [2021-02-03 09:31:42] Storing 17 MetaTraits
[INFO] [2021-02-03 09:31:42] Processing group of 17 in 1 groups of 1000
[INFO] [2021-02-03 09:31:42] Average Time: 0.0
[INFO] [2021-02-03 09:31:42] Total Time: 1s
[STOP] [2021-02-03 09:31:42] parse_diff_and_store
[START] [2021-02-03 09:31:42] resolve_keys
[INFO] [2021-02-03 09:31:47] Occurrences to nodes (through scientific_names)...
[INFO] [2021-02-03 09:31:47] traits to occurrences...
[INFO] [2021-02-03 09:31:47] traits to nodes (through occurrences)...
[INFO] [2021-02-03 09:31:47] Traits to sex term...
[INFO] [2021-02-03 09:31:47] Traits to lifestage term...
[INFO] [2021-02-03 09:31:47] MetaTraits to traits...
[INFO] [2021-02-03 09:31:47] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-02-03 09:31:47] Assocs to occurrences...
[INFO] [2021-02-03 09:31:47] Assocs to nodes...
[INFO] [2021-02-03 09:31:47] Assoc to sex term...
[INFO] [2021-02-03 09:31:47] Assoc to lifestage term...
[INFO] [2021-02-03 09:31:47] MetaAssoc to assocs...
[STOP] [2021-02-03 09:31:47] resolve_keys
[START] [2021-02-03 09:31:47] hold_for_later_1
[STOP] [2021-02-03 09:31:47] hold_for_later_1
[START] [2021-02-03 09:31:47] hold_for_later_2
[STOP] [2021-02-03 09:31:47] hold_for_later_2
[START] [2021-02-03 09:31:47] resolve_missing_parents
[STOP] [2021-02-03 09:31:47] resolve_missing_parents
[START] [2021-02-03 09:31:47] rebuild_nodes
[START] [2021-02-03 09:31:47] Flattener#flatten
[START] [2021-02-03 09:31:47] Flattener#study_resource
[START] [2021-02-03 09:31:47] Flattener#build_ancestry
[STOP] [2021-02-03 09:31:47] Flattener#build_ancestry
[INFO] [2021-02-03 09:31:47] 17 ancestry keys
[START] [2021-02-03 09:31:47] build_node_ancestors
[INFO] [2021-02-03 09:31:47] old ancestors deleted.
[STOP] [2021-02-03 09:31:47] build_node_ancestors
[WARN] [2021-02-03 09:31:47] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-02-03 09:31:47] Flattener#flatten
[STOP] [2021-02-03 09:31:47] rebuild_nodes
[START] [2021-02-03 09:31:47] resolve_missing_media_owners
[STOP] [2021-02-03 09:31:47] resolve_missing_media_owners
[START] [2021-02-03 09:31:47] sanitize_media_verbatims
[STOP] [2021-02-03 09:31:47] sanitize_media_verbatims
[START] [2021-02-03 09:31:47] queue_downloads
[STOP] [2021-02-03 09:31:47] queue_downloads
[START] [2021-02-03 09:31:47] parse_names
[WARN] [2021-02-03 09:31:47] I see 17 names which still need to be parsed.
[STOP] [2021-02-03 09:31:49] parse_names
[START] [2021-02-03 09:31:49] denormalize_canonical_names_to_nodes
[STOP] [2021-02-03 09:31:49] denormalize_canonical_names_to_nodes
[START] [2021-02-03 09:31:49] match_nodes
[START] [2021-02-03 09:31:49] map_all_nodes_to_pages
[STOP] [2021-02-03 09:31:49] map_all_nodes_to_pages
[INFO] [2021-02-03 09:31:49] ZERO unmatched nodes (of 17)! Nicely done.
[START] [2021-02-03 09:31:49] update_nodes
[STOP] [2021-02-03 09:31:49] update_nodes
[STOP] [2021-02-03 09:31:49] match_nodes
[START] [2021-02-03 09:31:49] reindex_search
[STOP] [2021-02-03 09:31:49] reindex_search
[START] [2021-02-03 09:31:49] normalize_units
[STOP] [2021-02-03 09:31:49] normalize_units
[START] [2021-02-03 09:31:49] calculate_statistics
[2021-02-03 09:31:49] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-02-03 09:31:49] calculate_statistics
[START] [2021-02-03 09:31:49] complete_harvest_instance
[START] [2021-02-03 09:31:49] overall_tsv_creation
[INFO] [2021-02-03 09:31:49] Processing group of 17 in 1 batches of 10000
[INFO] [2021-02-03 09:32:28] 17 Traits (unfiltered)...
[INFO] [2021-02-03 09:33:07] 17 Traits (filtered)...
[INFO] [2021-02-03 09:33:07] 0 Associations (filtered)...
[INFO] [2021-02-03 09:33:07] 34 metadata added.
[INFO] [2021-02-03 09:33:07] 0 metadata added.
[INFO] [2021-02-03 09:33:40] Average Time: 85.4
[INFO] [2021-02-03 09:33:40] Total Time: 1m52s
[STOP] [2021-02-03 09:33:40] overall_tsv_creation
[INFO] [2021-02-03 09:33:40] Done. Check your files:
[INFO] [2021-02-03 09:33:40] (17 lines) /app/public/data/ankel_simons_ank/publish_nodes.tsv
[INFO] [2021-02-03 09:33:40] (17 lines) /app/public/data/ankel_simons_ank/publish_scientific_names.tsv
[INFO] [2021-02-03 09:33:40] (18 lines) /app/public/data/ankel_simons_ank/publish_traits.tsv
[INFO] [2021-02-03 09:33:40] (35 lines) /app/public/data/ankel_simons_ank/publish_metadata.tsv
[STOP] [2021-02-03 09:33:40] complete_harvest_instance
[START] [2021-02-03 09:33:40] completed
[STOP] [2021-02-03 09:33:40] completed
[STOP] [2021-02-03 09:33:40] logged process, took 121.19
[INFO] [2021-04-06 17:52:35] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-06 17:52:36] ## remove_type: ScientificName
[INFO] [2021-04-06 17:52:36] ++ Calling delete_all on 17 instances...
[INFO] [2021-04-06 17:52:36] [17:52:36.059] Removed 17 Scientificnames
[INFO] [2021-04-06 17:52:36] ## remove_type: Vernacular
[INFO] [2021-04-06 17:52:36] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 17:52:36] [17:52:36.060] Removed 0 Vernaculars
[INFO] [2021-04-06 17:52:36] ## remove_type: Article
[INFO] [2021-04-06 17:52:36] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 17:52:36] [17:52:36.061] Removed 0 Articles
[INFO] [2021-04-06 17:52:36] ## remove_type: Medium
[INFO] [2021-04-06 17:52:36] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 17:52:36] [17:52:36.063] Removed 0 Media
[INFO] [2021-04-06 17:52:36] ## remove_type: Trait
[INFO] [2021-04-06 17:52:36] ++ Calling delete_all on 34 instances...
[INFO] [2021-04-06 17:52:36] [17:52:36.084] Removed 34 Traits
[INFO] [2021-04-06 17:52:36] ## remove_type: MetaTrait
[INFO] [2021-04-06 17:52:36] ++ Calling delete_all on 17 instances...
[INFO] [2021-04-06 17:52:36] [17:52:36.085] Removed 17 Metatraits
[INFO] [2021-04-06 17:52:36] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-06 17:52:36] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 17:52:36] [17:52:36.087] Removed 0 Occurrencemetadata
[INFO] [2021-04-06 17:52:36] ## remove_type: Assoc
[INFO] [2021-04-06 17:52:36] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 17:52:36] [17:52:36.088] Removed 0 Assocs
[INFO] [2021-04-06 17:52:36] ## remove_type: MetaAssoc
[INFO] [2021-04-06 17:52:36] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 17:52:36] [17:52:36.090] Removed 0 Metaassocs
[INFO] [2021-04-06 17:52:36] ## remove_type: Identifier
[INFO] [2021-04-06 17:52:36] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 17:52:36] [17:52:36.091] Removed 0 Identifiers
[INFO] [2021-04-06 17:52:36] ## remove_type: Reference
[INFO] [2021-04-06 17:52:36] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-06 17:52:36] [17:52:36.092] Removed 0 References
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728199...
[INFO] [2021-04-06 17:52:36] Starting batch with ID 87728195...
[INFO] [2021-04-06 17:52:36] ## remove_type: Node
[INFO] [2021-04-06 17:52:36] ++ Calling delete_all on 17 instances...
[INFO] [2021-04-06 17:52:36] [17:52:36.873] Removed 17 Nodes
[START] [2021-04-06 17:52:37] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-06 17:52:37] Creating resource from OpenData
[START] [2021-04-06 17:52:37] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-06 17:52:37] Parse meta.xml file and create formats with fields
[STOP] [2021-04-06 17:52:37] Parse meta.xml file and create formats with fields
[STOP] [2021-04-06 17:52:37] Creating resource from OpenData
[START] [2021-04-06 17:52:37] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-06 17:52:37] create_harvest_instance
[INFO] [2021-04-06 17:52:37] Created harvest instance #3652
[STOP] [2021-04-06 17:52:37] create_harvest_instance
[START] [2021-04-06 17:52:37] fetch_files
[STOP] [2021-04-06 17:52:37] fetch_files
[START] [2021-04-06 17:52:37] validate_each_file
[INFO] [2021-04-06 17:52:37] Looping over 3 formats...
[INFO] [2021-04-06 17:52:37] ...nodes (/app/public/data/ankel_simons_ank/taxa.txt)
[INFO] [2021-04-06 17:52:37] Valid: /app/public/converted_csv/ankel_simons_ank_nodes_3652.csv (17 lines)
[INFO] [2021-04-06 17:52:37] ...occurrences (/app/public/data/ankel_simons_ank/occurrences.txt)
[INFO] [2021-04-06 17:52:37] Valid: /app/public/converted_csv/ankel_simons_ank_occurrences_3652.csv (17 lines)
[INFO] [2021-04-06 17:52:37] ...measurements (/app/public/data/ankel_simons_ank/measurementsorfacts.txt)
[INFO] [2021-04-06 17:52:37] Valid: /app/public/converted_csv/ankel_simons_ank_measurements_3652.csv (34 lines)
[STOP] [2021-04-06 17:52:37] validate_each_file
[START] [2021-04-06 17:52:37] convert_to_csv
[INFO] [2021-04-06 17:52:37] Looping over 3 formats...
[INFO] [2021-04-06 17:52:37] ...nodes (/app/public/data/ankel_simons_ank/taxa.txt)
[CMD] [2021-04-06 17:52:37] /usr/bin/sort /app/public/converted_csv/ankel_simons_ank_nodes_3652.csv > /app/public/converted_csv/ankel_simons_ank_nodes_3652.csv_sorted
[INFO] [2021-04-06 17:52:37] Converted: /app/public/converted_csv/ankel_simons_ank_nodes_3652.csv (17 lines)
[INFO] [2021-04-06 17:52:37] ...occurrences (/app/public/data/ankel_simons_ank/occurrences.txt)
[CMD] [2021-04-06 17:52:37] /usr/bin/sort /app/public/converted_csv/ankel_simons_ank_occurrences_3652.csv > /app/public/converted_csv/ankel_simons_ank_occurrences_3652.csv_sorted
[INFO] [2021-04-06 17:52:37] Converted: /app/public/converted_csv/ankel_simons_ank_occurrences_3652.csv (17 lines)
[INFO] [2021-04-06 17:52:37] ...measurements (/app/public/data/ankel_simons_ank/measurementsorfacts.txt)
[CMD] [2021-04-06 17:52:37] /usr/bin/sort /app/public/converted_csv/ankel_simons_ank_measurements_3652.csv > /app/public/converted_csv/ankel_simons_ank_measurements_3652.csv_sorted
[INFO] [2021-04-06 17:52:37] Converted: /app/public/converted_csv/ankel_simons_ank_measurements_3652.csv (34 lines)
[STOP] [2021-04-06 17:52:37] convert_to_csv
[START] [2021-04-06 17:52:37] calculate_delta
[INFO] [2021-04-06 17:52:37] Looping over 3 formats...
[INFO] [2021-04-06 17:52:37] ...nodes (/app/public/data/ankel_simons_ank/taxa.txt)
[CMD] [2021-04-06 17:52:37] echo "0a" > /app/public/diff/ankel_simons_ank_nodes_3652.diff
[CMD] [2021-04-06 17:52:37] tail -n +1 /app/public/converted_csv/ankel_simons_ank_nodes_3652.csv >> /app/public/diff/ankel_simons_ank_nodes_3652.diff
[CMD] [2021-04-06 17:52:37] echo "." >> /app/public/diff/ankel_simons_ank_nodes_3652.diff
[INFO] [2021-04-06 17:52:37] Created diff: /app/public/diff/ankel_simons_ank_nodes_3652.diff (19 lines)
[INFO] [2021-04-06 17:52:37] ...occurrences (/app/public/data/ankel_simons_ank/occurrences.txt)
[CMD] [2021-04-06 17:52:37] echo "0a" > /app/public/diff/ankel_simons_ank_occurrences_3652.diff
[CMD] [2021-04-06 17:52:37] tail -n +1 /app/public/converted_csv/ankel_simons_ank_occurrences_3652.csv >> /app/public/diff/ankel_simons_ank_occurrences_3652.diff
[CMD] [2021-04-06 17:52:37] echo "." >> /app/public/diff/ankel_simons_ank_occurrences_3652.diff
[INFO] [2021-04-06 17:52:37] Created diff: /app/public/diff/ankel_simons_ank_occurrences_3652.diff (19 lines)
[INFO] [2021-04-06 17:52:37] ...measurements (/app/public/data/ankel_simons_ank/measurementsorfacts.txt)
[CMD] [2021-04-06 17:52:37] echo "0a" > /app/public/diff/ankel_simons_ank_measurements_3652.diff
[CMD] [2021-04-06 17:52:37] tail -n +1 /app/public/converted_csv/ankel_simons_ank_measurements_3652.csv >> /app/public/diff/ankel_simons_ank_measurements_3652.diff
[CMD] [2021-04-06 17:52:37] echo "." >> /app/public/diff/ankel_simons_ank_measurements_3652.diff
[INFO] [2021-04-06 17:52:37] Created diff: /app/public/diff/ankel_simons_ank_measurements_3652.diff (36 lines)
[STOP] [2021-04-06 17:52:37] calculate_delta
[START] [2021-04-06 17:52:37] parse_diff_and_store
[INFO] [2021-04-06 17:52:37] Handling diff: /app/public/diff/ankel_simons_ank_nodes_3652.diff (19 lines)
[INFO] [2021-04-06 17:52:37] Loading nodes diff file into memory (19 /app/public/diff/ankel_simons_ank_nodes_3652.diff lines)...
[INFO] [2021-04-06 17:52:37] Handling diff: /app/public/diff/ankel_simons_ank_occurrences_3652.diff (19 lines)
[INFO] [2021-04-06 17:52:37] Loading occurrences diff file into memory (19 /app/public/diff/ankel_simons_ank_occurrences_3652.diff lines)...
[INFO] [2021-04-06 17:52:37] Handling diff: /app/public/diff/ankel_simons_ank_measurements_3652.diff (36 lines)
[INFO] [2021-04-06 17:52:37] Loading measurements diff file into memory (36 /app/public/diff/ankel_simons_ank_measurements_3652.diff lines)...
[INFO] [2021-04-06 17:52:37] Storing 17 ScientificNames
[INFO] [2021-04-06 17:52:37] Processing group of 17 in 1 groups of 1000
[INFO] [2021-04-06 17:52:37] Average Time: 0.01
[INFO] [2021-04-06 17:52:37] Total Time: 1s
[INFO] [2021-04-06 17:52:37] Storing 17 Nodes
[INFO] [2021-04-06 17:52:37] Processing group of 17 in 1 groups of 1000
[INFO] [2021-04-06 17:52:37] Average Time: 0.01
[INFO] [2021-04-06 17:52:37] Total Time: 1s
[INFO] [2021-04-06 17:52:37] Storing 17 Occurrences
[INFO] [2021-04-06 17:52:37] Processing group of 17 in 1 groups of 1000
[INFO] [2021-04-06 17:52:37] Average Time: 0.0
[INFO] [2021-04-06 17:52:37] Total Time: 1s
[INFO] [2021-04-06 17:52:37] Storing 34 Traits
[INFO] [2021-04-06 17:52:37] Processing group of 34 in 1 groups of 1000
[INFO] [2021-04-06 17:52:37] Average Time: 0.01
[INFO] [2021-04-06 17:52:37] Total Time: 1s
[INFO] [2021-04-06 17:52:37] Storing 17 MetaTraits
[INFO] [2021-04-06 17:52:37] Processing group of 17 in 1 groups of 1000
[INFO] [2021-04-06 17:52:37] Average Time: 0.0
[INFO] [2021-04-06 17:52:37] Total Time: 1s
[STOP] [2021-04-06 17:52:37] parse_diff_and_store
[START] [2021-04-06 17:52:37] resolve_keys
[INFO] [2021-04-06 17:52:43] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-06 17:52:43] traits to occurrences...
[INFO] [2021-04-06 17:52:43] traits to nodes (through occurrences)...
[INFO] [2021-04-06 17:52:43] Traits to sex term...
[INFO] [2021-04-06 17:52:43] Traits to lifestage term...
[INFO] [2021-04-06 17:52:43] MetaTraits to traits...
[INFO] [2021-04-06 17:52:43] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-06 17:52:43] Assocs to occurrences...
[INFO] [2021-04-06 17:52:43] Assocs to nodes...
[INFO] [2021-04-06 17:52:43] Assoc to sex term...
[INFO] [2021-04-06 17:52:43] Assoc to lifestage term...
[INFO] [2021-04-06 17:52:43] MetaAssoc to assocs...
[STOP] [2021-04-06 17:52:43] resolve_keys
[START] [2021-04-06 17:52:43] hold_for_later_1
[STOP] [2021-04-06 17:52:43] hold_for_later_1
[START] [2021-04-06 17:52:43] hold_for_later_2
[STOP] [2021-04-06 17:52:43] hold_for_later_2
[START] [2021-04-06 17:52:43] resolve_missing_parents
[STOP] [2021-04-06 17:52:43] resolve_missing_parents
[START] [2021-04-06 17:52:43] rebuild_nodes
[START] [2021-04-06 17:52:43] Flattener#flatten
[START] [2021-04-06 17:52:43] Flattener#study_resource
[START] [2021-04-06 17:52:43] Flattener#build_ancestry
[STOP] [2021-04-06 17:52:43] Flattener#build_ancestry
[INFO] [2021-04-06 17:52:43] 17 ancestry keys
[START] [2021-04-06 17:52:43] build_node_ancestors
[INFO] [2021-04-06 17:52:43] old ancestors deleted.
[STOP] [2021-04-06 17:52:43] build_node_ancestors
[WARN] [2021-04-06 17:52:43] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-06 17:52:43] Flattener#flatten
[STOP] [2021-04-06 17:52:43] rebuild_nodes
[START] [2021-04-06 17:52:43] resolve_missing_media_owners
[STOP] [2021-04-06 17:52:43] resolve_missing_media_owners
[START] [2021-04-06 17:52:43] sanitize_media_verbatims
[STOP] [2021-04-06 17:52:43] sanitize_media_verbatims
[START] [2021-04-06 17:52:43] queue_downloads
[STOP] [2021-04-06 17:52:43] queue_downloads
[START] [2021-04-06 17:52:43] parse_names
[WARN] [2021-04-06 17:52:43] I see 17 names which still need to be parsed.
[STOP] [2021-04-06 17:52:44] parse_names
[START] [2021-04-06 17:52:44] denormalize_canonical_names_to_nodes
[STOP] [2021-04-06 17:52:44] denormalize_canonical_names_to_nodes
[START] [2021-04-06 17:52:44] match_nodes
[START] [2021-04-06 17:52:44] map_all_nodes_to_pages
[STOP] [2021-04-06 17:52:44] map_all_nodes_to_pages
[INFO] [2021-04-06 17:52:44] ZERO unmatched nodes (of 17)! Nicely done.
[START] [2021-04-06 17:52:44] update_nodes
[STOP] [2021-04-06 17:52:44] update_nodes
[STOP] [2021-04-06 17:52:44] match_nodes
[START] [2021-04-06 17:52:44] reindex_search
[STOP] [2021-04-06 17:52:44] reindex_search
[START] [2021-04-06 17:52:44] normalize_units
[STOP] [2021-04-06 17:52:44] normalize_units
[START] [2021-04-06 17:52:44] calculate_statistics
[2021-04-06 17:52:44] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-06 17:52:44] calculate_statistics
[START] [2021-04-06 17:52:44] complete_harvest_instance
[START] [2021-04-06 17:52:44] overall_tsv_creation
[INFO] [2021-04-06 17:52:44] Processing group of 17 in 1 batches of 10000
[INFO] [2021-04-06 17:53:21] 17 Traits (unfiltered)...
[INFO] [2021-04-06 17:53:56] 17 Traits (filtered)...
[INFO] [2021-04-06 17:53:56] 0 Associations (filtered)...
[INFO] [2021-04-06 17:53:56] 17 metadata added.
[INFO] [2021-04-06 17:53:56] 0 metadata added.
[INFO] [2021-04-06 17:54:23] Average Time: 73.83
[INFO] [2021-04-06 17:54:23] Total Time: 1m39s
[STOP] [2021-04-06 17:54:23] overall_tsv_creation
[INFO] [2021-04-06 17:54:23] Done. Check your files:
[INFO] [2021-04-06 17:54:23] (17 lines) /app/public/data/ankel_simons_ank/publish_nodes.tsv
[INFO] [2021-04-06 17:54:23] (17 lines) /app/public/data/ankel_simons_ank/publish_scientific_names.tsv
[INFO] [2021-04-06 17:54:23] (18 lines) /app/public/data/ankel_simons_ank/publish_traits.tsv
[INFO] [2021-04-06 17:54:23] (18 lines) /app/public/data/ankel_simons_ank/publish_metadata.tsv
[STOP] [2021-04-06 17:54:23] complete_harvest_instance
[START] [2021-04-06 17:54:23] completed
[STOP] [2021-04-06 17:54:23] completed
[STOP] [2021-04-06 17:54:23] logged process, took 106.27

Latest Process