Harvest for Robin et al 2018 Created 03 Aug 14:18

Harvesting Log

[INFO] [2022-08-03 14:18:26] Created harvest instance #4153
[STOP] [2022-08-03 14:18:26] create_harvest_instance
[START] [2022-08-03 14:18:26] fetch_files
[STOP] [2022-08-03 14:18:26] fetch_files
[START] [2022-08-03 14:18:26] validate_each_file
[INFO] [2022-08-03 14:18:26] Looping over 3 formats...
[INFO] [2022-08-03 14:18:26] ...nodes (/app/public/data/robin_et_al_robi/taxa.txt)
[INFO] [2022-08-03 14:18:27] Valid: /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_nodes_29425.csv (1 lines)
[INFO] [2022-08-03 14:18:27] ...occurrences (/app/public/data/robin_et_al_robi/occurrences.txt)
[INFO] [2022-08-03 14:18:27] Valid: /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_occurrences_29426.csv (1 lines)
[INFO] [2022-08-03 14:18:27] ...measurements (/app/public/data/robin_et_al_robi/measurementOrFact.txt)
[INFO] [2022-08-03 14:18:27] Valid: /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_measurements_29427.csv (2 lines)
[STOP] [2022-08-03 14:18:27] validate_each_file
[START] [2022-08-03 14:18:27] convert_to_csv
[INFO] [2022-08-03 14:18:27] Looping over 3 formats...
[INFO] [2022-08-03 14:18:27] ...nodes (/app/public/data/robin_et_al_robi/taxa.txt)
[CMD] [2022-08-03 14:18:27] /usr/bin/sort /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_nodes_29425.csv > /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_nodes_29425.csv_sorted
[INFO] [2022-08-03 14:18:27] Converted: /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_nodes_29425.csv (1 lines)
[INFO] [2022-08-03 14:18:27] ...occurrences (/app/public/data/robin_et_al_robi/occurrences.txt)
[CMD] [2022-08-03 14:18:27] /usr/bin/sort /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_occurrences_29426.csv > /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_occurrences_29426.csv_sorted
[INFO] [2022-08-03 14:18:27] Converted: /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_occurrences_29426.csv (1 lines)
[INFO] [2022-08-03 14:18:27] ...measurements (/app/public/data/robin_et_al_robi/measurementOrFact.txt)
[CMD] [2022-08-03 14:18:27] /usr/bin/sort /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_measurements_29427.csv > /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_measurements_29427.csv_sorted
[INFO] [2022-08-03 14:18:27] Converted: /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_measurements_29427.csv (2 lines)
[STOP] [2022-08-03 14:18:27] convert_to_csv
[START] [2022-08-03 14:18:27] calculate_delta
[INFO] [2022-08-03 14:18:27] Looping over 3 formats...
[INFO] [2022-08-03 14:18:27] ...nodes (/app/public/data/robin_et_al_robi/taxa.txt)
[CMD] [2022-08-03 14:18:27] echo "0a" > /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_nodes_29425.diff
[CMD] [2022-08-03 14:18:27] tail -n +1 /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_nodes_29425.csv >> /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_nodes_29425.diff
[CMD] [2022-08-03 14:18:27] echo "." >> /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_nodes_29425.diff
[INFO] [2022-08-03 14:18:27] Created diff: /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_nodes_29425.diff (3 lines)
[INFO] [2022-08-03 14:18:27] ...occurrences (/app/public/data/robin_et_al_robi/occurrences.txt)
[CMD] [2022-08-03 14:18:27] echo "0a" > /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_occurrences_29426.diff
[CMD] [2022-08-03 14:18:27] tail -n +1 /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_occurrences_29426.csv >> /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_occurrences_29426.diff
[CMD] [2022-08-03 14:18:27] echo "." >> /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_occurrences_29426.diff
[INFO] [2022-08-03 14:18:27] Created diff: /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_occurrences_29426.diff (3 lines)
[INFO] [2022-08-03 14:18:27] ...measurements (/app/public/data/robin_et_al_robi/measurementOrFact.txt)
[CMD] [2022-08-03 14:18:27] echo "0a" > /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_measurements_29427.diff
[CMD] [2022-08-03 14:18:27] tail -n +1 /app/public/data/robin_et_al_robi/converted_csv/robin_et_al_robi_measurements_29427.csv >> /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_measurements_29427.diff
[CMD] [2022-08-03 14:18:27] echo "." >> /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_measurements_29427.diff
[INFO] [2022-08-03 14:18:27] Created diff: /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_measurements_29427.diff (4 lines)
[STOP] [2022-08-03 14:18:27] calculate_delta
[START] [2022-08-03 14:18:27] parse_diff_and_store
[INFO] [2022-08-03 14:18:27] Handling diff: /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_nodes_29425.diff (3 lines)
[INFO] [2022-08-03 14:18:27] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-08-03 14:18:27] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-08-03 14:18:27] Storing 1 Nodes (2/1/3)
[INFO] [2022-08-03 14:18:27] Handling diff: /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_occurrences_29426.diff (3 lines)
[INFO] [2022-08-03 14:18:27] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-08-03 14:18:27] Storing 1 Occurrences (1/1/3)
[INFO] [2022-08-03 14:18:27] Handling diff: /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_measurements_29427.diff (4 lines)
[INFO] [2022-08-03 14:18:27] Loading measurements diff file into memory (4 lines)...
[STOP] [2022-08-03 14:18:28] parse_diff_and_store
[ERR] [2022-08-03 14:18:28] RuntimeError
[ERR] [2022-08-03 14:18:28] Missing Term for URI `https://www.wikidata.org/entity/Q7921571`, must be added!
[ERR] [2022-08-03 14:18:28] ../models/store/model_builder.rb:655:in `fail_on_bad_uri'
[ERR] [2022-08-03 14:18:28] ../models/store/model_builder.rb:609:in `convert_trait_value'
[ERR] [2022-08-03 14:18:28] ../models/store/model_builder.rb:427:in `build_trait'
[ERR] [2022-08-03 14:18:28] ../models/store/model_builder.rb:28:in `build_models'
[ERR] [2022-08-03 14:18:28] ../models/resource_harvester.rb:364:in `block (3 levels) in parse_diff_and_store'
[ERR] [2022-08-03 14:18:28] ../models/csv_parser.rb:111:in `block in diff_as_hashes'
[ERR] [2022-08-03 14:18:28] ../models/csv_parser.rb:28:in `block in line_at_a_time'
[ERR] [2022-08-03 14:18:28] ../models/csv_parser.rb:25:in `line_at_a_time'
[ERR] [2022-08-03 14:18:28] ../models/csv_parser.rb:96:in `diff_as_hashes'
[ERR] [2022-08-03 14:18:28] ../models/resource_harvester.rb:317:in `block (2 levels) in parse_diff_and_store'
[ERR] [2022-08-03 14:18:28] ../models/logged_process.rb:87:in `enter_group'
[ERR] [2022-08-03 14:18:28] ../models/resource_harvester.rb:316:in `block in parse_diff_and_store'
[ERR] [2022-08-03 14:18:28] ../models/resource_harvester.rb:772:in `block in each_diff'
[ERR] [2022-08-03 14:18:28] ../models/resource_harvester.rb:759:in `each_diff'
[ERR] [2022-08-03 14:18:28] ../models/resource_harvester.rb:308:in `parse_diff_and_store'
[ERR] [2022-08-03 14:18:28] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2022-08-03 14:18:28] ../models/logged_process.rb:43:in `run_step'
[ERR] [2022-08-03 14:18:28] ../models/resource_harvester.rb:86:in `block in start'
[ERR] [2022-08-03 14:18:28] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2022-08-03 14:18:28] ../models/resource_harvester.rb:75:in `start'
[ERR] [2022-08-03 14:18:28] ../models/resource.rb:300:in `harvest'
[ERR] [2022-08-03 14:18:28] bin/rails:4:in `require'
[ERR] [2022-08-03 14:18:28] bin/rails:4:in `<main>'
[STOP] [2022-08-03 14:18:28] logged process, took 2.12
[INFO] [2022-08-03 14:47:08] ## HARVEST: type = resume_harvest
[START] [2022-08-03 14:47:10] logged process: f6a4d92faad6f0e952536be37a712af291463456 Fix a bug causing an edless loop in TSV creation
[INFO] [2022-08-03 14:47:10] Already completed stage create_harvest_instance, skipping...
[INFO] [2022-08-03 14:47:10] Already completed stage fetch_files, skipping...
[INFO] [2022-08-03 14:47:10] Already completed stage validate_each_file, skipping...
[INFO] [2022-08-03 14:47:10] Already completed stage convert_to_csv, skipping...
[INFO] [2022-08-03 14:47:10] Already completed stage calculate_delta, skipping...
[START] [2022-08-03 14:47:10] parse_diff_and_store
[INFO] [2022-08-03 14:47:10] Handling diff: /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_nodes_29425.diff (3 lines)
[INFO] [2022-08-03 14:47:10] Loading nodes diff file into memory (3 lines)...
[WARN] [2022-08-03 14:47:11] SKIPPED 1 Scientific names (2/1/3) with resource_pks already be in the database!
[WARN] [2022-08-03 14:47:11] SKIPPED 1 Nodes (2/1/3) with resource_pks already be in the database!
[INFO] [2022-08-03 14:47:11] Storing 0 ScientificNames (2/1/3)
[WARN] [2022-08-03 14:47:11] No models to import, skipping!
[INFO] [2022-08-03 14:47:11] Storing 0 Nodes (2/1/3)
[WARN] [2022-08-03 14:47:11] No models to import, skipping!
[INFO] [2022-08-03 14:47:11] Handling diff: /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_occurrences_29426.diff (3 lines)
[INFO] [2022-08-03 14:47:11] Loading occurrences diff file into memory (3 lines)...
[WARN] [2022-08-03 14:47:11] SKIPPED 1 Occurrences (1/1/3) with resource_pks already be in the database!
[INFO] [2022-08-03 14:47:11] Storing 0 Occurrences (1/1/3)
[WARN] [2022-08-03 14:47:11] No models to import, skipping!
[INFO] [2022-08-03 14:47:11] Handling diff: /app/public/data/robin_et_al_robi/diff/robin_et_al_robi_measurements_29427.diff (4 lines)
[INFO] [2022-08-03 14:47:11] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-08-03 14:47:12] Storing 2 Traits (3/2/4)
[INFO] [2022-08-03 14:47:12] Storing 1 MetaTraits (3/2/4)
[STOP] [2022-08-03 14:47:12] parse_diff_and_store
[START] [2022-08-03 14:47:12] resolve_keys
[2022-08-03 14:47:12] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-03 14:47:19] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-03 14:47:19] traits to occurrences...
[INFO] [2022-08-03 14:47:19] traits to nodes (through occurrences)...
[INFO] [2022-08-03 14:47:19] Traits to sex term...
[INFO] [2022-08-03 14:47:19] Traits to lifestage term...
[INFO] [2022-08-03 14:47:19] MetaTraits to traits...
[INFO] [2022-08-03 14:47:19] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-03 14:47:19] Assocs to occurrences...
[INFO] [2022-08-03 14:47:19] Assocs to nodes...
[INFO] [2022-08-03 14:47:19] Assoc to sex term...
[INFO] [2022-08-03 14:47:19] Assoc to lifestage term...
[INFO] [2022-08-03 14:47:19] MetaAssoc to assocs...
[STOP] [2022-08-03 14:47:19] resolve_keys
[START] [2022-08-03 14:47:19] hold_for_later_1
[STOP] [2022-08-03 14:47:19] hold_for_later_1
[START] [2022-08-03 14:47:20] hold_for_later_2
[STOP] [2022-08-03 14:47:20] hold_for_later_2
[START] [2022-08-03 14:47:20] resolve_missing_parents
[STOP] [2022-08-03 14:47:20] resolve_missing_parents
[START] [2022-08-03 14:47:20] rebuild_nodes
[START] [2022-08-03 14:47:20] Flattener#flatten
[START] [2022-08-03 14:47:20] Flattener#study_resource
[START] [2022-08-03 14:47:20] Flattener#build_ancestry
[STOP] [2022-08-03 14:47:20] Flattener#build_ancestry
[INFO] [2022-08-03 14:47:20] 1 ancestry keys
[START] [2022-08-03 14:47:20] build_node_ancestors
[INFO] [2022-08-03 14:47:20] old ancestors deleted.
[STOP] [2022-08-03 14:47:20] build_node_ancestors
[WARN] [2022-08-03 14:47:20] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-03 14:47:20] Flattener#flatten
[STOP] [2022-08-03 14:47:20] rebuild_nodes
[START] [2022-08-03 14:47:20] resolve_missing_media_owners
[STOP] [2022-08-03 14:47:20] resolve_missing_media_owners
[START] [2022-08-03 14:47:20] sanitize_media_verbatims
[STOP] [2022-08-03 14:47:20] sanitize_media_verbatims
[START] [2022-08-03 14:47:20] queue_downloads
[STOP] [2022-08-03 14:47:20] queue_downloads
[START] [2022-08-03 14:47:20] parse_names
[WARN] [2022-08-03 14:47:20] I see 1 names which still need to be parsed.
[WARN] [2022-08-03 14:47:20] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-08-03 14:47:21] parse_names
[START] [2022-08-03 14:47:21] denormalize_canonical_names_to_nodes
[STOP] [2022-08-03 14:47:21] denormalize_canonical_names_to_nodes
[START] [2022-08-03 14:47:21] match_nodes
[START] [2022-08-03 14:47:21] map_all_nodes_to_pages
[STOP] [2022-08-03 14:47:21] map_all_nodes_to_pages
[INFO] [2022-08-03 14:47:21] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-08-03 14:47:21] update_nodes
[STOP] [2022-08-03 14:47:21] update_nodes
[STOP] [2022-08-03 14:47:21] match_nodes
[START] [2022-08-03 14:47:21] reindex_search
[STOP] [2022-08-03 14:47:21] reindex_search
[START] [2022-08-03 14:47:21] normalize_units
[STOP] [2022-08-03 14:47:21] normalize_units
[START] [2022-08-03 14:47:21] calculate_statistics
[2022-08-03 14:47:21] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-03 14:47:21] Duplicate page_id count: 0
[STOP] [2022-08-03 14:47:21] calculate_statistics
[START] [2022-08-03 14:47:21] complete_harvest_instance
[START] [2022-08-03 14:47:21] overall_tsv_creation
[INFO] [2022-08-03 14:47:21] Exporting 1 nodes as TSV in batches of 10000...
[INFO] [2022-08-03 14:47:21] Processing group of 1 in 1 batches of 10000
[INFO] [2022-08-03 14:48:03] 1 Traits (unfiltered) and 0 associations...
[INFO] [2022-08-03 14:48:03] Building Traits map for 1 nodes (this can take a while)...
[INFO] [2022-08-03 14:48:56] Mapped 1 traits (1 meta) for 1 nodes.
[INFO] [2022-08-03 14:48:56] Building Associations map (this can take a while)...
[INFO] [2022-08-03 14:48:56] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-03 14:48:56] Adding 1 traits...
[INFO] [2022-08-03 14:48:56] 1 metadata added.
[INFO] [2022-08-03 14:48:56] Adding 0 assocs...
[INFO] [2022-08-03 14:48:56] 0 metadata added.
[INFO] [2022-08-03 14:49:38] Processed 1/1 nodes
[INFO] [2022-08-03 14:49:38] Average Time: 110.89
[INFO] [2022-08-03 14:49:38] Total Time: 2m17s
[STOP] [2022-08-03 14:49:38] overall_tsv_creation
[INFO] [2022-08-03 14:49:38] Done. Check your files:
[INFO] [2022-08-03 14:49:38] (1 lines) /app/public/data/robin_et_al_robi/publish_nodes.tsv
[INFO] [2022-08-03 14:49:38] (1 lines) /app/public/data/robin_et_al_robi/publish_scientific_names.tsv
[INFO] [2022-08-03 14:49:38] (2 lines) /app/public/data/robin_et_al_robi/publish_traits.tsv
[INFO] [2022-08-03 14:49:38] (2 lines) /app/public/data/robin_et_al_robi/publish_metadata.tsv
[STOP] [2022-08-03 14:49:38] complete_harvest_instance
[START] [2022-08-03 14:49:38] completed
[STOP] [2022-08-03 14:49:38] completed
[STOP] [2022-08-03 14:49:38] logged process, took 147.31

Latest Process

03 Aug 14:47 EXITED currently processing 0