Stage:
fetch_files
Failed:
16 Jul 12:24
Completed:
16 Jul 12:24
Time to Harvest:
less than a minute
Harvesting Log
(138 lines)
# Logfile created on 2019-07-16 12:23:11 -0400 by logger.rb/56815
[START] [2019-07-16 12:23:11] logged process
[START] [2019-07-16 12:23:11] create_harvest_instance
[STOP] [2019-07-16 12:23:12] create_harvest_instance
[START] [2019-07-16 12:23:12] fetch_files
[STOP] [2019-07-16 12:23:12] fetch_files
[START] [2019-07-16 12:23:12] validate_each_file
[STOP] [2019-07-16 12:23:12] validate_each_file
[START] [2019-07-16 12:23:12] convert_to_csv
[CMD] [2019-07-16 12:23:12] /usr/bin/sort /app/public/converted_csv/osatp_agents_14233.csv > /app/public/converted_csv/osatp_agents_14233.csv_sorted
[CMD] [2019-07-16 12:23:13] /usr/bin/sort /app/public/converted_csv/osatp_nodes_14234.csv > /app/public/converted_csv/osatp_nodes_14234.csv_sorted
[CMD] [2019-07-16 12:23:15] /usr/bin/sort /app/public/converted_csv/osatp_media_14235.csv > /app/public/converted_csv/osatp_media_14235.csv_sorted
[STOP] [2019-07-16 12:23:17] convert_to_csv
[START] [2019-07-16 12:23:17] calculate_delta
[CMD] [2019-07-16 12:23:17] echo "0a" > /app/public/diff/osatp_agents_14233.diff
[CMD] [2019-07-16 12:23:18] tail -n +1 /app/public/converted_csv/osatp_agents_14233.csv >> /app/public/diff/osatp_agents_14233.diff
[CMD] [2019-07-16 12:23:20] echo "." >> /app/public/diff/osatp_agents_14233.diff
[CMD] [2019-07-16 12:23:22] echo "0a" > /app/public/diff/osatp_nodes_14234.diff
[CMD] [2019-07-16 12:23:23] tail -n +1 /app/public/converted_csv/osatp_nodes_14234.csv >> /app/public/diff/osatp_nodes_14234.diff
[CMD] [2019-07-16 12:23:25] echo "." >> /app/public/diff/osatp_nodes_14234.diff
[CMD] [2019-07-16 12:23:27] echo "0a" > /app/public/diff/osatp_media_14235.diff
[CMD] [2019-07-16 12:23:28] tail -n +1 /app/public/converted_csv/osatp_media_14235.csv >> /app/public/diff/osatp_media_14235.diff
[CMD] [2019-07-16 12:23:30] echo "." >> /app/public/diff/osatp_media_14235.diff
[STOP] [2019-07-16 12:23:32] calculate_delta
[START] [2019-07-16 12:23:32] parse_diff_and_store
[INFO] [2019-07-16 12:23:33] Loading agents diff file into memory (true lines)...
[INFO] [2019-07-16 12:23:35] Loading nodes diff file into memory (true lines)...
[INFO] [2019-07-16 12:23:37] Loading media diff file into memory (true lines)...
[INFO] [2019-07-16 12:23:37] Storing 3 Attributions
[INFO] [2019-07-16 12:23:37] Processing group of 3 in 1 groups of 1000
[INFO] [2019-07-16 12:23:37] Average Time: 0.0
[INFO] [2019-07-16 12:23:37] Total Time: 1s
[INFO] [2019-07-16 12:23:37] Storing 230 ScientificNames
[INFO] [2019-07-16 12:23:37] Processing group of 230 in 1 groups of 1000
[INFO] [2019-07-16 12:23:37] Average Time: 0.2
[INFO] [2019-07-16 12:23:37] Total Time: 1s
[INFO] [2019-07-16 12:23:37] Storing 230 Nodes
[INFO] [2019-07-16 12:23:37] Processing group of 230 in 1 groups of 1000
[INFO] [2019-07-16 12:23:37] Average Time: 0.08
[INFO] [2019-07-16 12:23:37] Total Time: 1s
[INFO] [2019-07-16 12:23:37] Storing 219 ContentAttributions
[INFO] [2019-07-16 12:23:37] Processing group of 219 in 1 groups of 1000
[INFO] [2019-07-16 12:23:37] Average Time: 0.1
[INFO] [2019-07-16 12:23:37] Total Time: 1s
[INFO] [2019-07-16 12:23:37] Storing 73 Media
[INFO] [2019-07-16 12:23:37] Processing group of 73 in 1 groups of 1000
[INFO] [2019-07-16 12:23:37] Average Time: 0.07
[INFO] [2019-07-16 12:23:37] Total Time: 1s
[STOP] [2019-07-16 12:23:37] parse_diff_and_store
[START] [2019-07-16 12:23:37] resolve_keys
[INFO] [2019-07-16 12:23:41] Occurrences to nodes (through scientific_names)...
[INFO] [2019-07-16 12:23:41] traits to occurrences...
[INFO] [2019-07-16 12:23:41] traits to nodes (through occurrences)...
[INFO] [2019-07-16 12:23:41] Traits to sex term...
[INFO] [2019-07-16 12:23:41] Traits to lifestage term...
[INFO] [2019-07-16 12:23:41] MetaTraits to traits...
[INFO] [2019-07-16 12:23:41] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-07-16 12:23:41] Assocs to occurrences...
[INFO] [2019-07-16 12:23:41] Assocs to nodes...
[INFO] [2019-07-16 12:23:41] Assoc to sex term...
[INFO] [2019-07-16 12:23:41] Assoc to lifestage term...
[STOP] [2019-07-16 12:23:41] resolve_keys
[START] [2019-07-16 12:23:41] hold_for_later_1
[STOP] [2019-07-16 12:23:41] hold_for_later_1
[START] [2019-07-16 12:23:41] hold_for_later_2
[STOP] [2019-07-16 12:23:41] hold_for_later_2
[START] [2019-07-16 12:23:41] resolve_missing_parents
[STOP] [2019-07-16 12:23:41] resolve_missing_parents
[START] [2019-07-16 12:23:41] rebuild_nodes
[START] [2019-07-16 12:23:41] Flattener#flatten
[START] [2019-07-16 12:23:41] Flattener#study_resource
[START] [2019-07-16 12:23:41] Flattener#build_ancestry
[STOP] [2019-07-16 12:23:41] Flattener#build_ancestry
[INFO] [2019-07-16 12:23:41] 230 ancestry keys
[START] [2019-07-16 12:23:41] build_node_ancestors
[INFO] [2019-07-16 12:23:41] old ancestors deleted.
[STOP] [2019-07-16 12:23:41] build_node_ancestors
[START] [2019-07-16 12:23:41] Flattener#propagate_ancestor_ids
[STOP] [2019-07-16 12:23:41] Flattener#propagate_ancestor_ids
[STOP] [2019-07-16 12:23:41] Flattener#flatten
[STOP] [2019-07-16 12:23:41] rebuild_nodes
[START] [2019-07-16 12:23:41] resolve_missing_media_owners
[STOP] [2019-07-16 12:23:41] resolve_missing_media_owners
[START] [2019-07-16 12:23:41] sanitize_media_verbatims
[STOP] [2019-07-16 12:23:41] sanitize_media_verbatims
[START] [2019-07-16 12:23:41] queue_downloads
[STOP] [2019-07-16 12:23:42] queue_downloads
[START] [2019-07-16 12:23:42] parse_names
[WARN] [2019-07-16 12:23:42] I see 230 names which still need to be parsed.
[STOP] [2019-07-16 12:23:43] parse_names
[START] [2019-07-16 12:23:43] denormalize_canonical_names_to_nodes
[STOP] [2019-07-16 12:23:43] denormalize_canonical_names_to_nodes
[START] [2019-07-16 12:23:43] match_nodes
[START] [2019-07-16 12:23:43] map_all_nodes_to_pages
[STOP] [2019-07-16 12:23:53] map_all_nodes_to_pages
[INFO] [2019-07-16 12:23:53] 15 Unmatched nodes (of 230)! That's too many to output. First 10: Pyrrophycophyta (#44581335); Calidris canutus rufa (#44581336); Leptothrix (#44581343); Leptothrix ochracea (#44581344); Bacillus subtilis (#44581349); Leptoptilos crumeniferus (#44581357); Korscheltellus (#44581382); Korscheltellus gracilis (#44581383); Leptoptilos crumeniferus (#44581396); Leptothrix ochracea (#44581402)
[START] [2019-07-16 12:23:53] update_nodes
[STOP] [2019-07-16 12:23:53] update_nodes
[STOP] [2019-07-16 12:23:53] match_nodes
[START] [2019-07-16 12:23:53] reindex_search
[STOP] [2019-07-16 12:23:53] reindex_search
[START] [2019-07-16 12:23:53] normalize_units
[STOP] [2019-07-16 12:23:53] normalize_units
[START] [2019-07-16 12:23:53] calculate_statistics
[STOP] [2019-07-16 12:23:53] calculate_statistics
[START] [2019-07-16 12:23:53] complete_harvest_instance
[START] [2019-07-16 12:23:53] overall_tsv_creation
[INFO] [2019-07-16 12:23:53] Processing group of 230 in 1 batches of 10000
[INFO] [2019-07-16 12:24:27] Average Time: 12.29
[INFO] [2019-07-16 12:24:27] Total Time: 34s
[STOP] [2019-07-16 12:24:27] overall_tsv_creation
[INFO] [2019-07-16 12:24:27] Done. Check your files:
[INFO] [2019-07-16 12:24:28] (230 lines) /app/public/data/osatp/publish_nodes.tsv
[INFO] [2019-07-16 12:24:30] (79 lines) /app/public/data/osatp/publish_node_ancestors.tsv
[INFO] [2019-07-16 12:24:32] (230 lines) /app/public/data/osatp/publish_scientific_names.tsv
[INFO] [2019-07-16 12:24:33] (73 lines) /app/public/data/osatp/publish_media.tsv
[INFO] [2019-07-16 12:24:35] (219 lines) /app/public/data/osatp/publish_attributions.tsv
[STOP] [2019-07-16 12:24:35] complete_harvest_instance
[START] [2019-07-16 12:24:35] completed
[STOP] [2019-07-16 12:24:35] completed
[STOP] [2019-07-16 12:24:35] logged process, took 83.76
[START] [2019-07-16 12:24:35] logged process
[START] [2019-07-16 12:24:35] create_harvest_instance
[STOP] [2019-07-16 12:24:35] create_harvest_instance
[START] [2019-07-16 12:24:35] fetch_files
[STOP] [2019-07-16 12:24:35] fetch_files
[ERR] [2019-07-16 12:24:35] RuntimeError
[ERR] [2019-07-16 12:24:35] No files have changed!
[ERR] [2019-07-16 12:24:35] ../models/resource_harvester.rb:115:in `fetch_files'
[ERR] [2019-07-16 12:24:35] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2019-07-16 12:24:35] ../models/logged_process.rb:19:in `run_step'
[ERR] [2019-07-16 12:24:35] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2019-07-16 12:24:35] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2019-07-16 12:24:35] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2019-07-16 12:24:35] ../models/resource.rb:134:in `lock'
[ERR] [2019-07-16 12:24:35] ../models/resource_harvester.rb:72:in `start'
[ERR] [2019-07-16 12:24:35] ../models/resource.rb:218:in `harvest'
[STOP] [2019-07-16 12:24:35] logged process, took 0.56
Latest Process