Harvest for Starko 2019 Created 25 Aug 14:48

Harvesting Log

[INFO] [2022-08-25 14:48:22] Created harvest instance #4203
[STOP] [2022-08-25 14:48:22] create_harvest_instance
[START] [2022-08-25 14:48:22] fetch_files
[STOP] [2022-08-25 14:48:22] fetch_files
[START] [2022-08-25 14:48:22] validate_each_file
[INFO] [2022-08-25 14:48:22] Created new folder: /app/public/converted_csv
[INFO] [2022-08-25 14:48:22] Looping over 3 formats...
[INFO] [2022-08-25 14:48:22] ...nodes (/app/public/data/starko_starko_20/taxa.txt)
[INFO] [2022-08-25 14:48:22] Valid: /app/public/data/starko_starko_20/converted_csv/starko_starko_20_nodes_29671.csv (2 lines)
[INFO] [2022-08-25 14:48:22] ...occurrences (/app/public/data/starko_starko_20/occurrences.txt)
[INFO] [2022-08-25 14:48:22] Valid: /app/public/data/starko_starko_20/converted_csv/starko_starko_20_occurrences_29672.csv (2 lines)
[INFO] [2022-08-25 14:48:22] ...measurements (/app/public/data/starko_starko_20/measurementOrFact.txt)
[INFO] [2022-08-25 14:48:22] Valid: /app/public/data/starko_starko_20/converted_csv/starko_starko_20_measurements_29673.csv (7 lines)
[STOP] [2022-08-25 14:48:22] validate_each_file
[START] [2022-08-25 14:48:22] convert_to_csv
[INFO] [2022-08-25 14:48:22] Looping over 3 formats...
[INFO] [2022-08-25 14:48:22] ...nodes (/app/public/data/starko_starko_20/taxa.txt)
[CMD] [2022-08-25 14:48:22] /usr/bin/sort /app/public/data/starko_starko_20/converted_csv/starko_starko_20_nodes_29671.csv > /app/public/data/starko_starko_20/converted_csv/starko_starko_20_nodes_29671.csv_sorted
[INFO] [2022-08-25 14:48:22] Converted: /app/public/data/starko_starko_20/converted_csv/starko_starko_20_nodes_29671.csv (2 lines)
[INFO] [2022-08-25 14:48:22] ...occurrences (/app/public/data/starko_starko_20/occurrences.txt)
[CMD] [2022-08-25 14:48:22] /usr/bin/sort /app/public/data/starko_starko_20/converted_csv/starko_starko_20_occurrences_29672.csv > /app/public/data/starko_starko_20/converted_csv/starko_starko_20_occurrences_29672.csv_sorted
[INFO] [2022-08-25 14:48:22] Converted: /app/public/data/starko_starko_20/converted_csv/starko_starko_20_occurrences_29672.csv (2 lines)
[INFO] [2022-08-25 14:48:22] ...measurements (/app/public/data/starko_starko_20/measurementOrFact.txt)
[CMD] [2022-08-25 14:48:22] /usr/bin/sort /app/public/data/starko_starko_20/converted_csv/starko_starko_20_measurements_29673.csv > /app/public/data/starko_starko_20/converted_csv/starko_starko_20_measurements_29673.csv_sorted
[INFO] [2022-08-25 14:48:22] Converted: /app/public/data/starko_starko_20/converted_csv/starko_starko_20_measurements_29673.csv (7 lines)
[STOP] [2022-08-25 14:48:22] convert_to_csv
[START] [2022-08-25 14:48:22] calculate_delta
[INFO] [2022-08-25 14:48:22] Created diff dir: /app/public/diff
[INFO] [2022-08-25 14:48:22] Looping over 3 formats...
[INFO] [2022-08-25 14:48:22] ...nodes (/app/public/data/starko_starko_20/taxa.txt)
[CMD] [2022-08-25 14:48:22] echo "0a" > /app/public/data/starko_starko_20/diff/starko_starko_20_nodes_29671.diff
[CMD] [2022-08-25 14:48:22] tail -n +1 /app/public/data/starko_starko_20/converted_csv/starko_starko_20_nodes_29671.csv >> /app/public/data/starko_starko_20/diff/starko_starko_20_nodes_29671.diff
[CMD] [2022-08-25 14:48:22] echo "." >> /app/public/data/starko_starko_20/diff/starko_starko_20_nodes_29671.diff
[INFO] [2022-08-25 14:48:22] Created diff: /app/public/data/starko_starko_20/diff/starko_starko_20_nodes_29671.diff (4 lines)
[INFO] [2022-08-25 14:48:22] ...occurrences (/app/public/data/starko_starko_20/occurrences.txt)
[CMD] [2022-08-25 14:48:22] echo "0a" > /app/public/data/starko_starko_20/diff/starko_starko_20_occurrences_29672.diff
[CMD] [2022-08-25 14:48:22] tail -n +1 /app/public/data/starko_starko_20/converted_csv/starko_starko_20_occurrences_29672.csv >> /app/public/data/starko_starko_20/diff/starko_starko_20_occurrences_29672.diff
[CMD] [2022-08-25 14:48:22] echo "." >> /app/public/data/starko_starko_20/diff/starko_starko_20_occurrences_29672.diff
[INFO] [2022-08-25 14:48:22] Created diff: /app/public/data/starko_starko_20/diff/starko_starko_20_occurrences_29672.diff (4 lines)
[INFO] [2022-08-25 14:48:22] ...measurements (/app/public/data/starko_starko_20/measurementOrFact.txt)
[CMD] [2022-08-25 14:48:22] echo "0a" > /app/public/data/starko_starko_20/diff/starko_starko_20_measurements_29673.diff
[CMD] [2022-08-25 14:48:22] tail -n +1 /app/public/data/starko_starko_20/converted_csv/starko_starko_20_measurements_29673.csv >> /app/public/data/starko_starko_20/diff/starko_starko_20_measurements_29673.diff
[CMD] [2022-08-25 14:48:22] echo "." >> /app/public/data/starko_starko_20/diff/starko_starko_20_measurements_29673.diff
[INFO] [2022-08-25 14:48:22] Created diff: /app/public/data/starko_starko_20/diff/starko_starko_20_measurements_29673.diff (9 lines)
[STOP] [2022-08-25 14:48:22] calculate_delta
[START] [2022-08-25 14:48:22] parse_diff_and_store
[INFO] [2022-08-25 14:48:22] Handling diff: /app/public/data/starko_starko_20/diff/starko_starko_20_nodes_29671.diff (4 lines)
[INFO] [2022-08-25 14:48:22] Loading nodes diff file into memory (4 lines)...
[INFO] [2022-08-25 14:48:22] Storing 2 ScientificNames (4/2/4)
[INFO] [2022-08-25 14:48:22] Storing 2 Nodes (4/2/4)
[INFO] [2022-08-25 14:48:23] Handling diff: /app/public/data/starko_starko_20/diff/starko_starko_20_occurrences_29672.diff (4 lines)
[INFO] [2022-08-25 14:48:23] Loading occurrences diff file into memory (4 lines)...
[INFO] [2022-08-25 14:48:23] Storing 2 Occurrences (2/2/4)
[INFO] [2022-08-25 14:48:23] Handling diff: /app/public/data/starko_starko_20/diff/starko_starko_20_measurements_29673.diff (9 lines)
[INFO] [2022-08-25 14:48:23] Loading measurements diff file into memory (9 lines)...
[STOP] [2022-08-25 14:48:24] parse_diff_and_store
[ERR] [2022-08-25 14:48:24] RuntimeError
[ERR] [2022-08-25 14:48:24] Missing Term for URI `http://purl.obolibrary.org/obo/GSSO_000904`, must be added!
[ERR] [2022-08-25 14:48:24] ../models/store/model_builder.rb:655:in `fail_on_bad_uri'
[ERR] [2022-08-25 14:48:24] ../models/store/model_builder.rb:609:in `convert_trait_value'
[ERR] [2022-08-25 14:48:24] ../models/store/model_builder.rb:427:in `build_trait'
[ERR] [2022-08-25 14:48:24] ../models/store/model_builder.rb:28:in `build_models'
[ERR] [2022-08-25 14:48:24] ../models/resource_harvester.rb:358:in `block (3 levels) in parse_diff_and_store'
[ERR] [2022-08-25 14:48:24] ../models/csv_parser.rb:111:in `block in diff_as_hashes'
[ERR] [2022-08-25 14:48:24] ../models/csv_parser.rb:28:in `block in line_at_a_time'
[ERR] [2022-08-25 14:48:24] ../models/csv_parser.rb:25:in `line_at_a_time'
[ERR] [2022-08-25 14:48:24] ../models/csv_parser.rb:96:in `diff_as_hashes'
[ERR] [2022-08-25 14:48:24] ../models/resource_harvester.rb:311:in `block (2 levels) in parse_diff_and_store'
[ERR] [2022-08-25 14:48:24] ../models/logged_process.rb:87:in `enter_group'
[ERR] [2022-08-25 14:48:24] ../models/resource_harvester.rb:310:in `block in parse_diff_and_store'
[ERR] [2022-08-25 14:48:24] ../models/resource_harvester.rb:765:in `block in each_diff'
[ERR] [2022-08-25 14:48:24] ../models/resource_harvester.rb:752:in `each_diff'
[ERR] [2022-08-25 14:48:24] ../models/resource_harvester.rb:302:in `parse_diff_and_store'
[ERR] [2022-08-25 14:48:24] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2022-08-25 14:48:24] ../models/logged_process.rb:43:in `run_step'
[ERR] [2022-08-25 14:48:24] ../models/resource_harvester.rb:86:in `block in start'
[ERR] [2022-08-25 14:48:24] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2022-08-25 14:48:24] ../models/resource_harvester.rb:75:in `start'
[ERR] [2022-08-25 14:48:24] ../models/resource.rb:300:in `harvest'
[ERR] [2022-08-25 14:48:24] ../models/resource.rb:276:in `re_download_opendata_and_harvest'
[ERR] [2022-08-25 14:48:24] bin/rails:4:in `require'
[ERR] [2022-08-25 14:48:24] bin/rails:4:in `<main>'
[STOP] [2022-08-25 14:48:24] logged process, took 2.03
[INFO] [2022-08-25 16:37:13] ## HARVEST: type = resume_harvest
[START] [2022-08-25 16:37:13] logged process: f73f353df9a1d1d5fe86620ddb421763ac872d1a Removed #check_for_duplicate_* on trait resources
[INFO] [2022-08-25 16:37:13] Already completed stage create_harvest_instance, skipping...
[INFO] [2022-08-25 16:37:13] Already completed stage fetch_files, skipping...
[INFO] [2022-08-25 16:37:13] Already completed stage validate_each_file, skipping...
[INFO] [2022-08-25 16:37:13] Already completed stage convert_to_csv, skipping...
[INFO] [2022-08-25 16:37:13] Already completed stage calculate_delta, skipping...
[START] [2022-08-25 16:37:13] parse_diff_and_store
[INFO] [2022-08-25 16:37:14] Handling diff: /app/public/data/starko_starko_20/diff/starko_starko_20_nodes_29671.diff (4 lines)
[INFO] [2022-08-25 16:37:14] Loading nodes diff file into memory (4 lines)...
[WARN] [2022-08-25 16:37:14] SKIPPED 2 Scientific names (4/2/4) with resource_pks already be in the database!
[WARN] [2022-08-25 16:37:14] SKIPPED 2 Nodes (4/2/4) with resource_pks already be in the database!
[INFO] [2022-08-25 16:37:14] Storing 0 ScientificNames (4/2/4)
[WARN] [2022-08-25 16:37:14] No models to import, skipping!
[INFO] [2022-08-25 16:37:14] Storing 0 Nodes (4/2/4)
[WARN] [2022-08-25 16:37:14] No models to import, skipping!
[INFO] [2022-08-25 16:37:14] Handling diff: /app/public/data/starko_starko_20/diff/starko_starko_20_occurrences_29672.diff (4 lines)
[INFO] [2022-08-25 16:37:14] Loading occurrences diff file into memory (4 lines)...
[WARN] [2022-08-25 16:37:14] SKIPPED 2 Occurrences (2/2/4) with resource_pks already be in the database!
[INFO] [2022-08-25 16:37:14] Storing 0 Occurrences (2/2/4)
[WARN] [2022-08-25 16:37:14] No models to import, skipping!
[INFO] [2022-08-25 16:37:14] Handling diff: /app/public/data/starko_starko_20/diff/starko_starko_20_measurements_29673.diff (9 lines)
[INFO] [2022-08-25 16:37:14] Loading measurements diff file into memory (9 lines)...
[INFO] [2022-08-25 16:37:15] Storing 7 Traits (10/7/9)
[INFO] [2022-08-25 16:37:15] Storing 3 MetaTraits (10/7/9)
[STOP] [2022-08-25 16:37:15] parse_diff_and_store
[START] [2022-08-25 16:37:15] resolve_keys
[2022-08-25 16:37:15] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-08-25 16:37:25] Occurrences to nodes (through scientific_names)...
[INFO] [2022-08-25 16:37:25] traits to occurrences...
[INFO] [2022-08-25 16:37:25] traits to nodes (through occurrences)...
[INFO] [2022-08-25 16:37:25] Traits to sex term...
[INFO] [2022-08-25 16:37:25] Traits to lifestage term...
[INFO] [2022-08-25 16:37:25] MetaTraits to traits...
[INFO] [2022-08-25 16:37:25] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-08-25 16:37:25] Assocs to occurrences...
[INFO] [2022-08-25 16:37:25] Assocs to nodes...
[INFO] [2022-08-25 16:37:25] Assoc to sex term...
[INFO] [2022-08-25 16:37:25] Assoc to lifestage term...
[INFO] [2022-08-25 16:37:25] MetaAssoc to assocs...
[STOP] [2022-08-25 16:37:25] resolve_keys
[START] [2022-08-25 16:37:25] hold_for_later_1
[STOP] [2022-08-25 16:37:25] hold_for_later_1
[START] [2022-08-25 16:37:25] hold_for_later_2
[STOP] [2022-08-25 16:37:25] hold_for_later_2
[START] [2022-08-25 16:37:25] resolve_missing_parents
[STOP] [2022-08-25 16:37:25] resolve_missing_parents
[START] [2022-08-25 16:37:25] rebuild_nodes
[START] [2022-08-25 16:37:25] Flattener#flatten
[START] [2022-08-25 16:37:25] Flattener#study_resource
[START] [2022-08-25 16:37:25] Flattener#build_ancestry
[STOP] [2022-08-25 16:37:25] Flattener#build_ancestry
[INFO] [2022-08-25 16:37:25] 2 ancestry keys
[START] [2022-08-25 16:37:25] build_node_ancestors
[INFO] [2022-08-25 16:37:25] old ancestors deleted.
[STOP] [2022-08-25 16:37:25] build_node_ancestors
[WARN] [2022-08-25 16:37:25] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-08-25 16:37:25] Flattener#flatten
[STOP] [2022-08-25 16:37:25] rebuild_nodes
[START] [2022-08-25 16:37:25] resolve_missing_media_owners
[STOP] [2022-08-25 16:37:25] resolve_missing_media_owners
[START] [2022-08-25 16:37:25] sanitize_media_verbatims
[STOP] [2022-08-25 16:37:25] sanitize_media_verbatims
[START] [2022-08-25 16:37:25] queue_downloads
[STOP] [2022-08-25 16:37:25] queue_downloads
[START] [2022-08-25 16:37:25] parse_names
[WARN] [2022-08-25 16:37:25] I see 2 names which still need to be parsed.
[WARN] [2022-08-25 16:37:25] Names to parse: 2 formatted: 2 learned: 2 parsed: 2
[STOP] [2022-08-25 16:37:26] parse_names
[START] [2022-08-25 16:37:26] denormalize_canonical_names_to_nodes
[STOP] [2022-08-25 16:37:26] denormalize_canonical_names_to_nodes
[START] [2022-08-25 16:37:26] match_nodes
[START] [2022-08-25 16:37:26] map_all_nodes_to_pages
[STOP] [2022-08-25 16:37:26] map_all_nodes_to_pages
[INFO] [2022-08-25 16:37:26] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2022-08-25 16:37:26] update_nodes
[STOP] [2022-08-25 16:37:26] update_nodes
[STOP] [2022-08-25 16:37:26] match_nodes
[START] [2022-08-25 16:37:26] reindex_search
[STOP] [2022-08-25 16:37:28] reindex_search
[START] [2022-08-25 16:37:28] normalize_units
[STOP] [2022-08-25 16:37:28] normalize_units
[START] [2022-08-25 16:37:28] calculate_statistics
[2022-08-25 16:37:28] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-08-25 16:37:28] Duplicate page_id count: 0
[STOP] [2022-08-25 16:37:28] calculate_statistics
[START] [2022-08-25 16:37:28] complete_harvest_instance
[START] [2022-08-25 16:37:28] overall_tsv_creation
[INFO] [2022-08-25 16:37:28] Processing group of 2 in 1 batches of 10000
[INFO] [2022-08-25 16:40:53] 3 Traits (unfiltered)...
[INFO] [2022-08-25 16:40:53] Building Traits map (this can take a while)...
[INFO] [2022-08-25 16:42:01] Done. 3 traits mapped (3 meta).
[INFO] [2022-08-25 16:42:01] Building Associations map (this can take a while)...
[INFO] [2022-08-25 16:42:01] Done. 0 assocs mapped (0 meta).
[INFO] [2022-08-25 16:42:01] Adding 3 traits...
[INFO] [2022-08-25 16:42:01] 4 metadata added.
[INFO] [2022-08-25 16:42:01] Adding 0 assocs...
[INFO] [2022-08-25 16:42:01] 0 metadata added.
[INFO] [2022-08-25 16:42:52] Average Time: 170.85
[INFO] [2022-08-25 16:42:52] Total Time: 5m25s
[STOP] [2022-08-25 16:42:52] overall_tsv_creation
[INFO] [2022-08-25 16:42:52] Done. Check your files:
[INFO] [2022-08-25 16:42:52] (2 lines) /app/public/data/starko_starko_20/publish_nodes.tsv
[INFO] [2022-08-25 16:42:52] (2 lines) /app/public/data/starko_starko_20/publish_scientific_names.tsv
[INFO] [2022-08-25 16:42:52] (4 lines) /app/public/data/starko_starko_20/publish_traits.tsv
[INFO] [2022-08-25 16:42:52] (5 lines) /app/public/data/starko_starko_20/publish_metadata.tsv
[STOP] [2022-08-25 16:42:52] complete_harvest_instance
[START] [2022-08-25 16:42:52] completed
[STOP] [2022-08-25 16:42:52] completed
[STOP] [2022-08-25 16:42:52] logged process, took 338.98

Latest Process

25 Aug 16:37 EXITED currently processing 0