Stage:
completed
Fetched:
12 Oct 02:16
Validated:
12 Oct 02:16
Deltas Created
12 Oct 02:16
Units Normalized:
12 Oct 02:19
Ancestry Built:
12 Oct 02:16
Nodes Matched:
12 Oct 02:19
Names Parsed:
12 Oct 02:16
New Models Stored:
12 Oct 02:16
Indexed:
12 Oct 02:19
Completed:
12 Oct 02:21
Time to Harvest:
less than a minute
Harvesting Log
(139 lines)
# Logfile created on 2019-10-12 02:16:18 -0400 by logger.rb/56815
[START] [2019-10-12 02:16:18] logged process
[START] [2019-10-12 02:16:18] create_harvest_instance
[STOP] [2019-10-12 02:16:19] create_harvest_instance
[START] [2019-10-12 02:16:19] fetch_files
[STOP] [2019-10-12 02:16:19] fetch_files
[START] [2019-10-12 02:16:19] validate_each_file
[STOP] [2019-10-12 02:16:19] validate_each_file
[START] [2019-10-12 02:16:19] convert_to_csv
[CMD] [2019-10-12 02:16:19] /usr/bin/sort /app/public/converted_csv/cayman_islands_s_refs_15387.csv > /app/public/converted_csv/cayman_islands_s_refs_15387.csv_sorted
[CMD] [2019-10-12 02:16:19] /usr/bin/sort /app/public/converted_csv/cayman_islands_s_nodes_15388.csv > /app/public/converted_csv/cayman_islands_s_nodes_15388.csv_sorted
[CMD] [2019-10-12 02:16:19] /usr/bin/sort /app/public/converted_csv/cayman_islands_s_occurrences_15389.csv > /app/public/converted_csv/cayman_islands_s_occurrences_15389.csv_sorted
[CMD] [2019-10-12 02:16:20] /usr/bin/sort /app/public/converted_csv/cayman_islands_s_measurements_15390.csv > /app/public/converted_csv/cayman_islands_s_measurements_15390.csv_sorted
[STOP] [2019-10-12 02:16:20] convert_to_csv
[START] [2019-10-12 02:16:20] calculate_delta
[CMD] [2019-10-12 02:16:20] echo "0a" > /app/public/diff/cayman_islands_s_refs_15387.diff
[CMD] [2019-10-12 02:16:20] tail -n +1 /app/public/converted_csv/cayman_islands_s_refs_15387.csv >> /app/public/diff/cayman_islands_s_refs_15387.diff
[CMD] [2019-10-12 02:16:20] echo "." >> /app/public/diff/cayman_islands_s_refs_15387.diff
[CMD] [2019-10-12 02:16:20] echo "0a" > /app/public/diff/cayman_islands_s_nodes_15388.diff
[CMD] [2019-10-12 02:16:20] tail -n +1 /app/public/converted_csv/cayman_islands_s_nodes_15388.csv >> /app/public/diff/cayman_islands_s_nodes_15388.diff
[CMD] [2019-10-12 02:16:20] echo "." >> /app/public/diff/cayman_islands_s_nodes_15388.diff
[CMD] [2019-10-12 02:16:20] echo "0a" > /app/public/diff/cayman_islands_s_occurrences_15389.diff
[CMD] [2019-10-12 02:16:20] tail -n +1 /app/public/converted_csv/cayman_islands_s_occurrences_15389.csv >> /app/public/diff/cayman_islands_s_occurrences_15389.diff
[CMD] [2019-10-12 02:16:20] echo "." >> /app/public/diff/cayman_islands_s_occurrences_15389.diff
[CMD] [2019-10-12 02:16:21] echo "0a" > /app/public/diff/cayman_islands_s_measurements_15390.diff
[CMD] [2019-10-12 02:16:21] tail -n +1 /app/public/converted_csv/cayman_islands_s_measurements_15390.csv >> /app/public/diff/cayman_islands_s_measurements_15390.diff
[CMD] [2019-10-12 02:16:21] echo "." >> /app/public/diff/cayman_islands_s_measurements_15390.diff
[STOP] [2019-10-12 02:16:21] calculate_delta
[START] [2019-10-12 02:16:21] parse_diff_and_store
[INFO] [2019-10-12 02:16:21] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 02:16:21] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 02:16:22] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 02:16:22] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 02:16:30] Storing 2 References
[INFO] [2019-10-12 02:16:30] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 02:16:30] Average Time: 0.0
[INFO] [2019-10-12 02:16:30] Total Time: 1s
[INFO] [2019-10-12 02:16:30] Storing 2638 ScientificNames
[INFO] [2019-10-12 02:16:30] Processing group of 2638 in 3 groups of 1000
[INFO] [2019-10-12 02:16:31] Average Time: 0.323
[INFO] [2019-10-12 02:16:31] Total Time: 1s
[INFO] [2019-10-12 02:16:31] Storing 2638 Nodes
[INFO] [2019-10-12 02:16:31] Processing group of 2638 in 3 groups of 1000
[INFO] [2019-10-12 02:16:32] Average Time: 0.287
[INFO] [2019-10-12 02:16:32] Total Time: 1s
[INFO] [2019-10-12 02:16:32] Storing 964 Occurrences
[INFO] [2019-10-12 02:16:32] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-12 02:16:32] Average Time: 0.13
[INFO] [2019-10-12 02:16:32] Total Time: 1s
[INFO] [2019-10-12 02:16:32] Storing 2600 TraitsReferences
[INFO] [2019-10-12 02:16:32] Processing group of 2600 in 3 groups of 1000
[INFO] [2019-10-12 02:16:33] Average Time: 0.093
[INFO] [2019-10-12 02:16:33] Total Time: 1s
[INFO] [2019-10-12 02:16:33] Storing 2599 Traits
[INFO] [2019-10-12 02:16:33] Processing group of 2599 in 3 groups of 1000
[INFO] [2019-10-12 02:16:34] Average Time: 0.317
[INFO] [2019-10-12 02:16:34] Total Time: 1s
[INFO] [2019-10-12 02:16:34] Storing 2600 MetaTraits
[INFO] [2019-10-12 02:16:34] Processing group of 2600 in 3 groups of 1000
[INFO] [2019-10-12 02:16:34] Average Time: 0.107
[INFO] [2019-10-12 02:16:34] Total Time: 1s
[STOP] [2019-10-12 02:16:34] parse_diff_and_store
[START] [2019-10-12 02:16:34] resolve_keys
[INFO] [2019-10-12 02:16:46] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 02:16:47] traits to occurrences...
[INFO] [2019-10-12 02:16:48] traits to nodes (through occurrences)...
[INFO] [2019-10-12 02:16:48] Traits to sex term...
[INFO] [2019-10-12 02:16:48] Traits to lifestage term...
[INFO] [2019-10-12 02:16:48] MetaTraits to traits...
[INFO] [2019-10-12 02:16:49] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 02:16:49] Assocs to occurrences...
[INFO] [2019-10-12 02:16:49] Assocs to nodes...
[INFO] [2019-10-12 02:16:49] Assoc to sex term...
[INFO] [2019-10-12 02:16:49] Assoc to lifestage term...
[STOP] [2019-10-12 02:16:49] resolve_keys
[START] [2019-10-12 02:16:49] hold_for_later_1
[STOP] [2019-10-12 02:16:49] hold_for_later_1
[START] [2019-10-12 02:16:49] hold_for_later_2
[STOP] [2019-10-12 02:16:49] hold_for_later_2
[START] [2019-10-12 02:16:49] resolve_missing_parents
[STOP] [2019-10-12 02:16:53] resolve_missing_parents
[START] [2019-10-12 02:16:53] rebuild_nodes
[START] [2019-10-12 02:16:53] Flattener#flatten
[START] [2019-10-12 02:16:53] Flattener#study_resource
[START] [2019-10-12 02:16:53] Flattener#build_ancestry
[STOP] [2019-10-12 02:16:53] Flattener#build_ancestry
[INFO] [2019-10-12 02:16:53] 2638 ancestry keys
[START] [2019-10-12 02:16:53] build_node_ancestors
[INFO] [2019-10-12 02:16:53] old ancestors deleted.
[STOP] [2019-10-12 02:16:54] build_node_ancestors
[START] [2019-10-12 02:16:54] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 02:16:54] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 02:16:54] Flattener#flatten
[STOP] [2019-10-12 02:16:54] rebuild_nodes
[START] [2019-10-12 02:16:54] resolve_missing_media_owners
[STOP] [2019-10-12 02:16:54] resolve_missing_media_owners
[START] [2019-10-12 02:16:54] sanitize_media_verbatims
[STOP] [2019-10-12 02:16:54] sanitize_media_verbatims
[START] [2019-10-12 02:16:54] queue_downloads
[STOP] [2019-10-12 02:16:54] queue_downloads
[START] [2019-10-12 02:16:54] parse_names
[WARN] [2019-10-12 02:16:54] I see 2638 names which still need to be parsed.
[STOP] [2019-10-12 02:16:57] parse_names
[START] [2019-10-12 02:16:57] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 02:16:57] denormalize_canonical_names_to_nodes
[START] [2019-10-12 02:16:57] match_nodes
[START] [2019-10-12 02:16:57] map_all_nodes_to_pages
[STOP] [2019-10-12 02:19:10] map_all_nodes_to_pages
[INFO] [2019-10-12 02:19:10] 118 Unmatched nodes (of 2638)! That's too many to output. First 10: Coerebidae (#49086135); Seiurus noveboracensis (#49087623); Oreothlypis peregrina (#49086411); Oreothlypis celata (#49088567); Oreothlypis ruficapilla (#49088672); Dendroica (#49086636); Dendroica petechia (#49086635); Dendroica striata (#49088109); Dendroica palmarum (#49088368); Tiaris olivacea (#49087235)
[START] [2019-10-12 02:19:10] update_nodes
[STOP] [2019-10-12 02:19:11] update_nodes
[STOP] [2019-10-12 02:19:11] match_nodes
[START] [2019-10-12 02:19:11] reindex_search
[STOP] [2019-10-12 02:19:16] reindex_search
[START] [2019-10-12 02:19:16] normalize_units
[STOP] [2019-10-12 02:19:16] normalize_units
[START] [2019-10-12 02:19:16] calculate_statistics
[STOP] [2019-10-12 02:19:16] calculate_statistics
[START] [2019-10-12 02:19:16] complete_harvest_instance
[START] [2019-10-12 02:19:16] overall_tsv_creation
[INFO] [2019-10-12 02:19:16] Processing group of 2638 in 1 batches of 10000
[INFO] [2019-10-12 02:20:12] 964 Traits (unfiltered)...
[INFO] [2019-10-12 02:20:26] 964 Traits (filtered)...
[INFO] [2019-10-12 02:20:26] 0 Associations (filtered)...
[INFO] [2019-10-12 02:21:04] 4820 metadata added.
[INFO] [2019-10-12 02:21:04] 0 metadata added.
[INFO] [2019-10-12 02:21:04] Average Time: 86.14
[INFO] [2019-10-12 02:21:04] Total Time: 1m49s
[STOP] [2019-10-12 02:21:04] overall_tsv_creation
[INFO] [2019-10-12 02:21:04] Done. Check your files:
[INFO] [2019-10-12 02:21:05] (2638 lines) /app/public/data/cayman_islands_s/publish_nodes.tsv
[INFO] [2019-10-12 02:21:05] (7447 lines) /app/public/data/cayman_islands_s/publish_node_ancestors.tsv
[INFO] [2019-10-12 02:21:05] (2638 lines) /app/public/data/cayman_islands_s/publish_scientific_names.tsv
[INFO] [2019-10-12 02:21:05] (965 lines) /app/public/data/cayman_islands_s/publish_traits.tsv
[INFO] [2019-10-12 02:21:05] (4821 lines) /app/public/data/cayman_islands_s/publish_metadata.tsv
[STOP] [2019-10-12 02:21:05] complete_harvest_instance
[START] [2019-10-12 02:21:05] completed
[STOP] [2019-10-12 02:21:05] completed
[STOP] [2019-10-12 02:21:05] logged process, took 286.61
Latest Process