Harvest for Chan 2010 Created 08 Sep 16:16

Harvesting Log

[INFO] [2022-09-08 16:16:04] Created harvest instance #4211
[STOP] [2022-09-08 16:16:04] create_harvest_instance
[START] [2022-09-08 16:16:04] fetch_files
[STOP] [2022-09-08 16:16:04] fetch_files
[START] [2022-09-08 16:16:04] validate_each_file
[INFO] [2022-09-08 16:16:04] Looping over 4 formats...
[INFO] [2022-09-08 16:16:04] ...refs (/app/public/data/chan_chan_2010/references.tsv)
[INFO] [2022-09-08 16:16:05] Valid: /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_refs_29696.csv (0 lines)
[INFO] [2022-09-08 16:16:05] ...nodes (/app/public/data/chan_chan_2010/taxa.txt)
[INFO] [2022-09-08 16:16:05] Valid: /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_nodes_29693.csv (1 lines)
[INFO] [2022-09-08 16:16:05] ...occurrences (/app/public/data/chan_chan_2010/occurrences.txt)
[INFO] [2022-09-08 16:16:05] Valid: /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_occurrences_29694.csv (1 lines)
[INFO] [2022-09-08 16:16:05] ...measurements (/app/public/data/chan_chan_2010/measurementsorfacts.txt)
[INFO] [2022-09-08 16:16:05] Valid: /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_measurements_29695.csv (2 lines)
[STOP] [2022-09-08 16:16:05] validate_each_file
[START] [2022-09-08 16:16:05] convert_to_csv
[INFO] [2022-09-08 16:16:05] Looping over 4 formats...
[INFO] [2022-09-08 16:16:05] ...refs (/app/public/data/chan_chan_2010/references.tsv)
[CMD] [2022-09-08 16:16:05] /usr/bin/sort /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_refs_29696.csv > /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_refs_29696.csv_sorted
[INFO] [2022-09-08 16:16:05] Converted: /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_refs_29696.csv (0 lines)
[INFO] [2022-09-08 16:16:05] ...nodes (/app/public/data/chan_chan_2010/taxa.txt)
[CMD] [2022-09-08 16:16:05] /usr/bin/sort /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_nodes_29693.csv > /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_nodes_29693.csv_sorted
[INFO] [2022-09-08 16:16:05] Converted: /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_nodes_29693.csv (1 lines)
[INFO] [2022-09-08 16:16:05] ...occurrences (/app/public/data/chan_chan_2010/occurrences.txt)
[CMD] [2022-09-08 16:16:05] /usr/bin/sort /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_occurrences_29694.csv > /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_occurrences_29694.csv_sorted
[INFO] [2022-09-08 16:16:05] Converted: /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_occurrences_29694.csv (1 lines)
[INFO] [2022-09-08 16:16:05] ...measurements (/app/public/data/chan_chan_2010/measurementsorfacts.txt)
[CMD] [2022-09-08 16:16:05] /usr/bin/sort /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_measurements_29695.csv > /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_measurements_29695.csv_sorted
[INFO] [2022-09-08 16:16:05] Converted: /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_measurements_29695.csv (2 lines)
[STOP] [2022-09-08 16:16:05] convert_to_csv
[START] [2022-09-08 16:16:05] calculate_delta
[INFO] [2022-09-08 16:16:05] Looping over 4 formats...
[INFO] [2022-09-08 16:16:05] ...refs (/app/public/data/chan_chan_2010/references.tsv)
[CMD] [2022-09-08 16:16:05] echo "0a" > /app/public/data/chan_chan_2010/diff/chan_chan_2010_refs_29696.diff
[CMD] [2022-09-08 16:16:05] tail -n +1 /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_refs_29696.csv >> /app/public/data/chan_chan_2010/diff/chan_chan_2010_refs_29696.diff
[CMD] [2022-09-08 16:16:05] echo "." >> /app/public/data/chan_chan_2010/diff/chan_chan_2010_refs_29696.diff
[INFO] [2022-09-08 16:16:05] Created diff: /app/public/data/chan_chan_2010/diff/chan_chan_2010_refs_29696.diff (2 lines)
[INFO] [2022-09-08 16:16:05] ...nodes (/app/public/data/chan_chan_2010/taxa.txt)
[CMD] [2022-09-08 16:16:05] echo "0a" > /app/public/data/chan_chan_2010/diff/chan_chan_2010_nodes_29693.diff
[CMD] [2022-09-08 16:16:05] tail -n +1 /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_nodes_29693.csv >> /app/public/data/chan_chan_2010/diff/chan_chan_2010_nodes_29693.diff
[CMD] [2022-09-08 16:16:05] echo "." >> /app/public/data/chan_chan_2010/diff/chan_chan_2010_nodes_29693.diff
[INFO] [2022-09-08 16:16:05] Created diff: /app/public/data/chan_chan_2010/diff/chan_chan_2010_nodes_29693.diff (3 lines)
[INFO] [2022-09-08 16:16:05] ...occurrences (/app/public/data/chan_chan_2010/occurrences.txt)
[CMD] [2022-09-08 16:16:05] echo "0a" > /app/public/data/chan_chan_2010/diff/chan_chan_2010_occurrences_29694.diff
[CMD] [2022-09-08 16:16:05] tail -n +1 /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_occurrences_29694.csv >> /app/public/data/chan_chan_2010/diff/chan_chan_2010_occurrences_29694.diff
[CMD] [2022-09-08 16:16:05] echo "." >> /app/public/data/chan_chan_2010/diff/chan_chan_2010_occurrences_29694.diff
[INFO] [2022-09-08 16:16:05] Created diff: /app/public/data/chan_chan_2010/diff/chan_chan_2010_occurrences_29694.diff (3 lines)
[INFO] [2022-09-08 16:16:05] ...measurements (/app/public/data/chan_chan_2010/measurementsorfacts.txt)
[CMD] [2022-09-08 16:16:05] echo "0a" > /app/public/data/chan_chan_2010/diff/chan_chan_2010_measurements_29695.diff
[CMD] [2022-09-08 16:16:05] tail -n +1 /app/public/data/chan_chan_2010/converted_csv/chan_chan_2010_measurements_29695.csv >> /app/public/data/chan_chan_2010/diff/chan_chan_2010_measurements_29695.diff
[CMD] [2022-09-08 16:16:05] echo "." >> /app/public/data/chan_chan_2010/diff/chan_chan_2010_measurements_29695.diff
[INFO] [2022-09-08 16:16:05] Created diff: /app/public/data/chan_chan_2010/diff/chan_chan_2010_measurements_29695.diff (4 lines)
[STOP] [2022-09-08 16:16:05] calculate_delta
[START] [2022-09-08 16:16:05] parse_diff_and_store
[INFO] [2022-09-08 16:16:05] Handling diff: /app/public/data/chan_chan_2010/diff/chan_chan_2010_refs_29696.diff (2 lines)
[INFO] [2022-09-08 16:16:05] Loading refs diff file into memory (2 lines)...
[INFO] [2022-09-08 16:16:05] Handling diff: /app/public/data/chan_chan_2010/diff/chan_chan_2010_nodes_29693.diff (3 lines)
[INFO] [2022-09-08 16:16:05] Loading nodes diff file into memory (3 lines)...
[INFO] [2022-09-08 16:16:05] Storing 1 ScientificNames (2/1/3)
[INFO] [2022-09-08 16:16:05] Storing 1 Nodes (2/1/3)
[INFO] [2022-09-08 16:16:05] Handling diff: /app/public/data/chan_chan_2010/diff/chan_chan_2010_occurrences_29694.diff (3 lines)
[INFO] [2022-09-08 16:16:05] Loading occurrences diff file into memory (3 lines)...
[INFO] [2022-09-08 16:16:05] Storing 1 Occurrences (1/1/3)
[INFO] [2022-09-08 16:16:05] Handling diff: /app/public/data/chan_chan_2010/diff/chan_chan_2010_measurements_29695.diff (4 lines)
[INFO] [2022-09-08 16:16:05] Loading measurements diff file into memory (4 lines)...
[INFO] [2022-09-08 16:16:05] Storing 2 Traits (3/2/4)
[INFO] [2022-09-08 16:16:05] Storing 1 MetaTraits (3/2/4)
[STOP] [2022-09-08 16:16:05] parse_diff_and_store
[START] [2022-09-08 16:16:05] resolve_keys
[2022-09-08 16:16:05] Resolving downloaded urls (this is not actually downloading them yet)
[INFO] [2022-09-08 16:16:18] Occurrences to nodes (through scientific_names)...
[INFO] [2022-09-08 16:16:18] traits to occurrences...
[INFO] [2022-09-08 16:16:18] traits to nodes (through occurrences)...
[INFO] [2022-09-08 16:16:18] Traits to sex term...
[INFO] [2022-09-08 16:16:18] Traits to lifestage term...
[INFO] [2022-09-08 16:16:18] MetaTraits to traits...
[INFO] [2022-09-08 16:16:18] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2022-09-08 16:16:18] Assocs to occurrences...
[INFO] [2022-09-08 16:16:18] Assocs to nodes...
[INFO] [2022-09-08 16:16:18] Assoc to sex term...
[INFO] [2022-09-08 16:16:18] Assoc to lifestage term...
[INFO] [2022-09-08 16:16:18] MetaAssoc to assocs...
[STOP] [2022-09-08 16:16:18] resolve_keys
[START] [2022-09-08 16:16:18] hold_for_later_1
[STOP] [2022-09-08 16:16:18] hold_for_later_1
[START] [2022-09-08 16:16:18] hold_for_later_2
[STOP] [2022-09-08 16:16:18] hold_for_later_2
[START] [2022-09-08 16:16:18] resolve_missing_parents
[STOP] [2022-09-08 16:16:18] resolve_missing_parents
[START] [2022-09-08 16:16:18] rebuild_nodes
[START] [2022-09-08 16:16:18] Flattener#flatten
[START] [2022-09-08 16:16:18] Flattener#study_resource
[START] [2022-09-08 16:16:18] Flattener#build_ancestry
[STOP] [2022-09-08 16:16:18] Flattener#build_ancestry
[INFO] [2022-09-08 16:16:18] 1 ancestry keys
[START] [2022-09-08 16:16:18] build_node_ancestors
[INFO] [2022-09-08 16:16:18] old ancestors deleted.
[STOP] [2022-09-08 16:16:18] build_node_ancestors
[WARN] [2022-09-08 16:16:18] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2022-09-08 16:16:18] Flattener#flatten
[STOP] [2022-09-08 16:16:18] rebuild_nodes
[START] [2022-09-08 16:16:18] resolve_missing_media_owners
[STOP] [2022-09-08 16:16:18] resolve_missing_media_owners
[START] [2022-09-08 16:16:18] sanitize_media_verbatims
[STOP] [2022-09-08 16:16:18] sanitize_media_verbatims
[START] [2022-09-08 16:16:18] queue_downloads
[STOP] [2022-09-08 16:16:18] queue_downloads
[START] [2022-09-08 16:16:18] parse_names
[WARN] [2022-09-08 16:16:18] I see 1 names which still need to be parsed.
[WARN] [2022-09-08 16:16:18] Names to parse: 1 formatted: 1 learned: 1 parsed: 1
[STOP] [2022-09-08 16:16:19] parse_names
[START] [2022-09-08 16:16:19] denormalize_canonical_names_to_nodes
[STOP] [2022-09-08 16:16:19] denormalize_canonical_names_to_nodes
[START] [2022-09-08 16:16:19] match_nodes
[START] [2022-09-08 16:16:19] map_all_nodes_to_pages
[STOP] [2022-09-08 16:16:19] map_all_nodes_to_pages
[INFO] [2022-09-08 16:16:19] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2022-09-08 16:16:19] update_nodes
[STOP] [2022-09-08 16:16:19] update_nodes
[STOP] [2022-09-08 16:16:19] match_nodes
[START] [2022-09-08 16:16:19] reindex_search
[STOP] [2022-09-08 16:16:20] reindex_search
[START] [2022-09-08 16:16:20] normalize_units
[STOP] [2022-09-08 16:16:20] normalize_units
[START] [2022-09-08 16:16:20] calculate_statistics
[2022-09-08 16:16:20] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[INFO] [2022-09-08 16:16:20] Duplicate page_id count: 0
[STOP] [2022-09-08 16:16:20] calculate_statistics
[START] [2022-09-08 16:16:20] complete_harvest_instance
[START] [2022-09-08 16:16:20] overall_tsv_creation
[STOP] [2022-09-08 16:16:20] overall_tsv_creation
[STOP] [2022-09-08 16:16:20] complete_harvest_instance
[ERR] [2022-09-08 16:16:20] ActiveRecord::StatementInvalid
[ERR] [2022-09-08 16:16:20] Mysql2::Error::ConnectionError: Lost connection to MySQL server during query: SELECT id FROM `resources` WHERE repository_id = 1003 LIMIT 1
[ERR] [2022-09-08 16:16:20] ../models/web_db.rb:290:in `exec_query'
[ERR] [2022-09-08 16:16:20] ../models/web_db.rb:267:in `find_by_repo_id'
[ERR] [2022-09-08 16:16:20] ../models/web_db.rb:225:in `resource_id'
[ERR] [2022-09-08 16:16:20] ../models/publisher.rb:99:in `learn_resource_publishing_id'
[ERR] [2022-09-08 16:16:20] ../models/publisher.rb:78:in `block in by_resource'
[ERR] [2022-09-08 16:16:20] ../models/logged_process.rb:43:in `run_step'
[ERR] [2022-09-08 16:16:20] ../models/publisher.rb:77:in `by_resource'
[ERR] [2022-09-08 16:16:20] ../models/publisher.rb:21:in `by_resource'
[ERR] [2022-09-08 16:16:20] ../models/resource_harvester.rb:720:in `complete_harvest_instance'
[ERR] [2022-09-08 16:16:20] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2022-09-08 16:16:20] ../models/logged_process.rb:43:in `run_step'
[ERR] [2022-09-08 16:16:20] ../models/resource_harvester.rb:86:in `block in start'
[ERR] [2022-09-08 16:16:20] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2022-09-08 16:16:20] ../models/resource_harvester.rb:75:in `start'
[ERR] [2022-09-08 16:16:20] ../models/resource.rb:300:in `harvest'
[ERR] [2022-09-08 16:16:20] ../models/resource.rb:276:in `re_download_opendata_and_harvest'
[ERR] [2022-09-08 16:16:20] bin/rails:4:in `require'
[ERR] [2022-09-08 16:16:20] bin/rails:4:in `<main>'
[STOP] [2022-09-08 16:16:20] logged process, took 15.39
[INFO] [2022-09-08 16:17:29] ## HARVEST: type = resume_harvest
[START] [2022-09-08 16:17:30] logged process: f73f353df9a1d1d5fe86620ddb421763ac872d1a Removed #check_for_duplicate_* on trait resources
[INFO] [2022-09-08 16:17:30] Already completed stage create_harvest_instance, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage fetch_files, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage validate_each_file, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage convert_to_csv, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage calculate_delta, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage parse_diff_and_store, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage resolve_keys, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage hold_for_later_1, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage hold_for_later_2, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage resolve_missing_parents, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage rebuild_nodes, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage resolve_missing_media_owners, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage sanitize_media_verbatims, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage queue_downloads, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage parse_names, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage denormalize_canonical_names_to_nodes, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage match_nodes, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage reindex_search, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage normalize_units, skipping...
[INFO] [2022-09-08 16:17:30] Already completed stage calculate_statistics, skipping...
[START] [2022-09-08 16:17:30] complete_harvest_instance
[START] [2022-09-08 16:17:30] overall_tsv_creation
[INFO] [2022-09-08 16:17:30] Processing group of 1 in 1 batches of 10000
[INFO] [2022-09-08 16:19:00] 1 Traits (unfiltered)...
[INFO] [2022-09-08 16:19:00] Building Traits map (this can take a while)...
[INFO] [2022-09-08 16:20:01] Done. 1 traits mapped (1 meta).
[INFO] [2022-09-08 16:20:01] Building Associations map (this can take a while)...
[INFO] [2022-09-08 16:20:01] Done. 0 assocs mapped (0 meta).
[INFO] [2022-09-08 16:20:01] Adding 1 traits...
[INFO] [2022-09-08 16:20:01] 1 metadata added.
[INFO] [2022-09-08 16:20:01] Adding 0 assocs...
[INFO] [2022-09-08 16:20:01] 0 metadata added.
[INFO] [2022-09-08 16:20:50] Average Time: 138.84
[INFO] [2022-09-08 16:20:50] Total Time: 3m21s
[STOP] [2022-09-08 16:20:50] overall_tsv_creation
[INFO] [2022-09-08 16:20:50] Done. Check your files:
[INFO] [2022-09-08 16:20:50] (1 lines) /app/public/data/chan_chan_2010/publish_nodes.tsv
[INFO] [2022-09-08 16:20:50] (1 lines) /app/public/data/chan_chan_2010/publish_scientific_names.tsv
[INFO] [2022-09-08 16:20:50] (2 lines) /app/public/data/chan_chan_2010/publish_traits.tsv
[INFO] [2022-09-08 16:20:50] (2 lines) /app/public/data/chan_chan_2010/publish_metadata.tsv
[STOP] [2022-09-08 16:20:51] complete_harvest_instance
[START] [2022-09-08 16:20:51] completed
[STOP] [2022-09-08 16:20:51] completed
[STOP] [2022-09-08 16:20:51] logged process, took 200.58

Latest Process

08 Sep 16:16 EXITED currently processing 0