Stage:
completed
Fetched:
02 Oct 12:03
Validated:
02 Oct 12:03
Deltas Created
02 Oct 12:03
Units Normalized:
11 Oct 14:07
Ancestry Built:
02 Oct 12:08
Nodes Matched:
02 Oct 12:45
Names Parsed:
02 Oct 12:08
New Models Stored:
02 Oct 12:05
Indexed:
11 Oct 14:07
Completed:
11 Oct 14:14
Time to Harvest:
less than a minute
Harvesting Log
(194 lines)
# Logfile created on 2019-10-02 12:03:10 -0400 by logger.rb/56815
[START] [2019-10-02 12:03:10] logged process
[START] [2019-10-02 12:03:10] create_harvest_instance
[STOP] [2019-10-02 12:03:10] create_harvest_instance
[START] [2019-10-02 12:03:10] fetch_files
[STOP] [2019-10-02 12:03:10] fetch_files
[START] [2019-10-02 12:03:10] validate_each_file
[STOP] [2019-10-02 12:03:13] validate_each_file
[START] [2019-10-02 12:03:13] convert_to_csv
[CMD] [2019-10-02 12:03:13] /usr/bin/sort /app/public/converted_csv/belgium_sp_list_refs_14994.csv > /app/public/converted_csv/belgium_sp_list_refs_14994.csv_sorted
[CMD] [2019-10-02 12:03:14] /usr/bin/sort /app/public/converted_csv/belgium_sp_list_nodes_14995.csv > /app/public/converted_csv/belgium_sp_list_nodes_14995.csv_sorted
[CMD] [2019-10-02 12:03:16] /usr/bin/sort /app/public/converted_csv/belgium_sp_list_occurrences_14996.csv > /app/public/converted_csv/belgium_sp_list_occurrences_14996.csv_sorted
[CMD] [2019-10-02 12:03:17] /usr/bin/sort /app/public/converted_csv/belgium_sp_list_measurements_14997.csv > /app/public/converted_csv/belgium_sp_list_measurements_14997.csv_sorted
[STOP] [2019-10-02 12:03:19] convert_to_csv
[START] [2019-10-02 12:03:19] calculate_delta
[CMD] [2019-10-02 12:03:19] echo "0a" > /app/public/diff/belgium_sp_list_refs_14994.diff
[CMD] [2019-10-02 12:03:20] tail -n +1 /app/public/converted_csv/belgium_sp_list_refs_14994.csv >> /app/public/diff/belgium_sp_list_refs_14994.diff
[CMD] [2019-10-02 12:03:22] echo "." >> /app/public/diff/belgium_sp_list_refs_14994.diff
[CMD] [2019-10-02 12:03:23] echo "0a" > /app/public/diff/belgium_sp_list_nodes_14995.diff
[CMD] [2019-10-02 12:03:25] tail -n +1 /app/public/converted_csv/belgium_sp_list_nodes_14995.csv >> /app/public/diff/belgium_sp_list_nodes_14995.diff
[CMD] [2019-10-02 12:03:26] echo "." >> /app/public/diff/belgium_sp_list_nodes_14995.diff
[CMD] [2019-10-02 12:03:28] echo "0a" > /app/public/diff/belgium_sp_list_occurrences_14996.diff
[CMD] [2019-10-02 12:03:29] tail -n +1 /app/public/converted_csv/belgium_sp_list_occurrences_14996.csv >> /app/public/diff/belgium_sp_list_occurrences_14996.diff
[CMD] [2019-10-02 12:03:31] echo "." >> /app/public/diff/belgium_sp_list_occurrences_14996.diff
[CMD] [2019-10-02 12:03:32] echo "0a" > /app/public/diff/belgium_sp_list_measurements_14997.diff
[CMD] [2019-10-02 12:03:34] tail -n +1 /app/public/converted_csv/belgium_sp_list_measurements_14997.csv >> /app/public/diff/belgium_sp_list_measurements_14997.diff
[CMD] [2019-10-02 12:03:35] echo "." >> /app/public/diff/belgium_sp_list_measurements_14997.diff
[STOP] [2019-10-02 12:03:37] calculate_delta
[START] [2019-10-02 12:03:37] parse_diff_and_store
[INFO] [2019-10-02 12:03:38] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-02 12:03:40] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-02 12:03:49] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-02 12:03:52] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-02 12:05:08] Storing 2 References
[INFO] [2019-10-02 12:05:08] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-02 12:05:09] Average Time: 0.0
[INFO] [2019-10-02 12:05:09] Total Time: 1s
[INFO] [2019-10-02 12:05:09] Storing 22227 ScientificNames
[INFO] [2019-10-02 12:05:09] Processing group of 22227 in 23 groups of 1000
[INFO] [2019-10-02 12:05:17] Average Time: 0.356
[INFO] [2019-10-02 12:05:17] Total Time: 9s
[INFO] [2019-10-02 12:05:17] last 3 / first 3: 0.72
[INFO] [2019-10-02 12:05:17] Std.Dev: 0.1224744871391589; Max: 0.81
[INFO] [2019-10-02 12:05:17] Storing 22227 Nodes
[INFO] [2019-10-02 12:05:17] Processing group of 22227 in 23 groups of 1000
[INFO] [2019-10-02 12:05:23] Average Time: 0.276
[INFO] [2019-10-02 12:05:23] Total Time: 7s
[INFO] [2019-10-02 12:05:23] last 3 / first 3: 0.81
[INFO] [2019-10-02 12:05:23] Std.Dev: 0.044721359549995794; Max: 0.33
[INFO] [2019-10-02 12:05:23] Storing 13978 Occurrences
[INFO] [2019-10-02 12:05:23] Processing group of 13978 in 14 groups of 1000
[INFO] [2019-10-02 12:05:25] Average Time: 0.124
[INFO] [2019-10-02 12:05:25] Total Time: 2s
[INFO] [2019-10-02 12:05:25] last 3 / first 3: 1.84
[INFO] [2019-10-02 12:05:25] Std.Dev: 0.03162277660168379; Max: 0.21
[INFO] [2019-10-02 12:05:25] Storing 28042 TraitsReferences
[INFO] [2019-10-02 12:05:25] Processing group of 28042 in 29 groups of 1000
[INFO] [2019-10-02 12:05:28] Average Time: 0.086
[INFO] [2019-10-02 12:05:28] Total Time: 3s
[INFO] [2019-10-02 12:05:28] last 3 / first 3: 0.37
[INFO] [2019-10-02 12:05:28] Std.Dev: 0.05477225575051661; Max: 0.35
[INFO] [2019-10-02 12:05:28] Storing 28041 Traits
[INFO] [2019-10-02 12:05:28] Processing group of 28041 in 29 groups of 1000
[INFO] [2019-10-02 12:05:37] Average Time: 0.329
[INFO] [2019-10-02 12:05:37] Total Time: 10s
[INFO] [2019-10-02 12:05:37] last 3 / first 3: 0.58
[INFO] [2019-10-02 12:05:37] Std.Dev: 0.11832159566199232; Max: 0.7
[INFO] [2019-10-02 12:05:37] Storing 28020 MetaTraits
[INFO] [2019-10-02 12:05:37] Processing group of 28020 in 29 groups of 1000
[INFO] [2019-10-02 12:05:41] Average Time: 0.122
[INFO] [2019-10-02 12:05:41] Total Time: 4s
[INFO] [2019-10-02 12:05:41] last 3 / first 3: 0.65
[INFO] [2019-10-02 12:05:41] Std.Dev: 0.03162277660168379; Max: 0.19
[STOP] [2019-10-02 12:05:41] parse_diff_and_store
[START] [2019-10-02 12:05:41] resolve_keys
[INFO] [2019-10-02 12:06:49] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-02 12:06:55] traits to occurrences...
[INFO] [2019-10-02 12:07:03] traits to nodes (through occurrences)...
[INFO] [2019-10-02 12:07:04] Traits to sex term...
[INFO] [2019-10-02 12:07:10] Traits to lifestage term...
[INFO] [2019-10-02 12:07:17] MetaTraits to traits...
[INFO] [2019-10-02 12:07:19] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-02 12:07:23] Assocs to occurrences...
[INFO] [2019-10-02 12:07:23] Assocs to nodes...
[INFO] [2019-10-02 12:07:23] Assoc to sex term...
[INFO] [2019-10-02 12:07:23] Assoc to lifestage term...
[STOP] [2019-10-02 12:07:23] resolve_keys
[START] [2019-10-02 12:07:23] hold_for_later_1
[STOP] [2019-10-02 12:07:23] hold_for_later_1
[START] [2019-10-02 12:07:23] hold_for_later_2
[STOP] [2019-10-02 12:07:23] hold_for_later_2
[START] [2019-10-02 12:07:23] resolve_missing_parents
[STOP] [2019-10-02 12:07:55] resolve_missing_parents
[START] [2019-10-02 12:07:55] rebuild_nodes
[START] [2019-10-02 12:07:55] Flattener#flatten
[START] [2019-10-02 12:07:55] Flattener#study_resource
[START] [2019-10-02 12:07:55] Flattener#build_ancestry
[STOP] [2019-10-02 12:07:57] Flattener#build_ancestry
[INFO] [2019-10-02 12:07:57] 22227 ancestry keys
[START] [2019-10-02 12:07:57] build_node_ancestors
[INFO] [2019-10-02 12:07:57] old ancestors deleted.
[STOP] [2019-10-02 12:08:02] build_node_ancestors
[START] [2019-10-02 12:08:07] Flattener#propagate_ancestor_ids
[STOP] [2019-10-02 12:08:09] Flattener#propagate_ancestor_ids
[STOP] [2019-10-02 12:08:09] Flattener#flatten
[STOP] [2019-10-02 12:08:09] rebuild_nodes
[START] [2019-10-02 12:08:09] resolve_missing_media_owners
[STOP] [2019-10-02 12:08:09] resolve_missing_media_owners
[START] [2019-10-02 12:08:09] sanitize_media_verbatims
[STOP] [2019-10-02 12:08:09] sanitize_media_verbatims
[START] [2019-10-02 12:08:09] queue_downloads
[STOP] [2019-10-02 12:08:09] queue_downloads
[START] [2019-10-02 12:08:09] parse_names
[WARN] [2019-10-02 12:08:09] I see 22227 names which still need to be parsed.
[STOP] [2019-10-02 12:08:26] parse_names
[START] [2019-10-02 12:08:26] denormalize_canonical_names_to_nodes
[STOP] [2019-10-02 12:08:26] denormalize_canonical_names_to_nodes
[START] [2019-10-02 12:08:26] match_nodes
[START] [2019-10-02 12:08:26] map_all_nodes_to_pages
[STOP] [2019-10-02 12:45:22] map_all_nodes_to_pages
[INFO] [2019-10-02 12:45:22] 2996 Unmatched nodes (of 22227)! That's too many to output. First 10: Larus melanocephalus (#47740264); Larus argenteus (#47757664); Thalaseus (#47745247); Thalaseus sandvicensis (#47745246); Philomachus (#47739258); Philomachus pugnax (#47739257); Limicola (#47757136); Limicola falcinellus (#47757135); Anas strepera (#47737962); Anas clypeata (#47738084)
[START] [2019-10-02 12:45:22] update_nodes
[STOP] [2019-10-02 12:45:29] update_nodes
[STOP] [2019-10-02 12:45:29] match_nodes
[START] [2019-10-02 12:45:29] reindex_search
[STOP] [2019-10-02 12:46:01] reindex_search
[ERR] [2019-10-02 12:46:01] Faraday::TimeoutError
[ERR] [2019-10-02 12:46:01] Net::ReadTimeout
[ERR] [2019-10-02 12:46:01] ../models/resource_harvester.rb:615:in `reindex_search'
[ERR] [2019-10-02 12:46:01] ../models/resource_harvester.rb:86:in `block (3 levels) in start'
[ERR] [2019-10-02 12:46:01] ../models/logged_process.rb:19:in `run_step'
[ERR] [2019-10-02 12:46:01] ../models/resource_harvester.rb:86:in `block (2 levels) in start'
[ERR] [2019-10-02 12:46:01] ../models/resource_harvester.rb:75:in `each_key'
[ERR] [2019-10-02 12:46:01] ../models/resource_harvester.rb:75:in `block in start'
[ERR] [2019-10-02 12:46:01] ../models/resource.rb:139:in `lock'
[ERR] [2019-10-02 12:46:01] ../models/resource_harvester.rb:72:in `start'
[ERR] [2019-10-02 12:46:01] ../models/resource.rb:223:in `harvest'
[ERR] [2019-10-02 12:46:01] ../models/resource.rb:199:in `re_download_opendata_and_harvest'
[STOP] [2019-10-02 12:46:01] logged process, took 2571.47
[START] [2019-10-11 14:07:08] logged process
[INFO] [2019-10-11 14:07:08] Already completed stage create_harvest_instance, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage fetch_files, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage validate_each_file, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage convert_to_csv, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage calculate_delta, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage parse_diff_and_store, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage resolve_keys, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage hold_for_later_1, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage hold_for_later_2, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage resolve_missing_parents, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage rebuild_nodes, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage resolve_missing_media_owners, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage sanitize_media_verbatims, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage queue_downloads, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage parse_names, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage denormalize_canonical_names_to_nodes, skipping...
[INFO] [2019-10-11 14:07:08] Already completed stage match_nodes, skipping...
[START] [2019-10-11 14:07:08] reindex_search
[STOP] [2019-10-11 14:07:49] reindex_search
[START] [2019-10-11 14:07:49] normalize_units
[STOP] [2019-10-11 14:07:49] normalize_units
[START] [2019-10-11 14:07:49] calculate_statistics
[STOP] [2019-10-11 14:07:49] calculate_statistics
[START] [2019-10-11 14:07:49] complete_harvest_instance
[START] [2019-10-11 14:07:49] overall_tsv_creation
[INFO] [2019-10-11 14:07:49] Processing group of 22227 in 3 batches of 10000
[INFO] [2019-10-11 14:09:17] 5999 Traits (unfiltered)...
[INFO] [2019-10-11 14:09:31] 5999 Traits (filtered)...
[INFO] [2019-10-11 14:09:31] 0 Associations (filtered)...
[INFO] [2019-10-11 14:10:21] 29991 metadata added.
[INFO] [2019-10-11 14:10:21] 0 metadata added.
[INFO] [2019-10-11 14:11:51] 6449 Traits (unfiltered)...
[INFO] [2019-10-11 14:12:05] 6449 Traits (filtered)...
[INFO] [2019-10-11 14:12:05] 0 Associations (filtered)...
[INFO] [2019-10-11 14:12:58] 32229 metadata added.
[INFO] [2019-10-11 14:12:58] 0 metadata added.
[INFO] [2019-10-11 14:13:55] 1530 Traits (unfiltered)...
[INFO] [2019-10-11 14:14:09] 1530 Traits (filtered)...
[INFO] [2019-10-11 14:14:09] 0 Associations (filtered)...
[INFO] [2019-10-11 14:14:49] 7648 metadata added.
[INFO] [2019-10-11 14:14:49] 0 metadata added.
[INFO] [2019-10-11 14:14:49] Average Time: 115.38
[INFO] [2019-10-11 14:14:49] Total Time: 6m60s
[STOP] [2019-10-11 14:14:49] overall_tsv_creation
[INFO] [2019-10-11 14:14:49] Done. Check your files:
[INFO] [2019-10-11 14:14:49] (22227 lines) /app/public/data/belgium_sp_list/publish_nodes.tsv
[INFO] [2019-10-11 14:14:49] (74322 lines) /app/public/data/belgium_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-11 14:14:49] (22227 lines) /app/public/data/belgium_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-11 14:14:49] (13979 lines) /app/public/data/belgium_sp_list/publish_traits.tsv
[INFO] [2019-10-11 14:14:49] (69869 lines) /app/public/data/belgium_sp_list/publish_metadata.tsv
[STOP] [2019-10-11 14:14:49] complete_harvest_instance
[START] [2019-10-11 14:14:49] completed
[STOP] [2019-10-11 14:14:49] completed
[STOP] [2019-10-11 14:14:49] logged process, took 460.81
Latest Process