Harvest for Great Australian Bight Species List Created 23 Dec 02:20

Stage: completed
Fetched: 23 Dec 02:20
Validated: 23 Dec 02:20
Deltas Created 23 Dec 02:20
Units Normalized: 23 Dec 03:13
Ancestry Built: 23 Dec 02:22
Nodes Matched: 23 Dec 03:12
Names Parsed: 23 Dec 02:23
New Models Stored: 23 Dec 02:21
Indexed: 23 Dec 03:13
Completed: 23 Dec 03:17
Time to Harvest: 1 minute
Harvesting Log

(156 lines)
# Logfile created on 2019-12-23 02:20:12 -0500 by logger.rb/56815
[START] [2019-12-23 02:20:12] logged process
[START] [2019-12-23 02:20:12] create_harvest_instance
[STOP] [2019-12-23 02:20:13] create_harvest_instance
[START] [2019-12-23 02:20:13] fetch_files
[STOP] [2019-12-23 02:20:13] fetch_files
[START] [2019-12-23 02:20:13] validate_each_file
[STOP] [2019-12-23 02:20:14] validate_each_file
[START] [2019-12-23 02:20:14] convert_to_csv
[CMD] [2019-12-23 02:20:14] /usr/bin/sort /app/public/converted_csv/gabsl_refs_19242.csv > /app/public/converted_csv/gabsl_refs_19242.csv_sorted
[CMD] [2019-12-23 02:20:14] /usr/bin/sort /app/public/converted_csv/gabsl_nodes_19243.csv > /app/public/converted_csv/gabsl_nodes_19243.csv_sorted
[CMD] [2019-12-23 02:20:14] /usr/bin/sort /app/public/converted_csv/gabsl_occurrences_19244.csv > /app/public/converted_csv/gabsl_occurrences_19244.csv_sorted
[CMD] [2019-12-23 02:20:14] /usr/bin/sort /app/public/converted_csv/gabsl_measurements_19245.csv > /app/public/converted_csv/gabsl_measurements_19245.csv_sorted
[STOP] [2019-12-23 02:20:14] convert_to_csv
[START] [2019-12-23 02:20:14] calculate_delta
[CMD] [2019-12-23 02:20:14] echo "0a" > /app/public/diff/gabsl_refs_19242.diff
[CMD] [2019-12-23 02:20:14] tail -n +1 /app/public/converted_csv/gabsl_refs_19242.csv >> /app/public/diff/gabsl_refs_19242.diff
[CMD] [2019-12-23 02:20:14] echo "." >> /app/public/diff/gabsl_refs_19242.diff
[CMD] [2019-12-23 02:20:15] echo "0a" > /app/public/diff/gabsl_nodes_19243.diff
[CMD] [2019-12-23 02:20:15] tail -n +1 /app/public/converted_csv/gabsl_nodes_19243.csv >> /app/public/diff/gabsl_nodes_19243.diff
[CMD] [2019-12-23 02:20:15] echo "." >> /app/public/diff/gabsl_nodes_19243.diff
[CMD] [2019-12-23 02:20:15] echo "0a" > /app/public/diff/gabsl_occurrences_19244.diff
[CMD] [2019-12-23 02:20:15] tail -n +1 /app/public/converted_csv/gabsl_occurrences_19244.csv >> /app/public/diff/gabsl_occurrences_19244.diff
[CMD] [2019-12-23 02:20:15] echo "." >> /app/public/diff/gabsl_occurrences_19244.diff
[CMD] [2019-12-23 02:20:15] echo "0a" > /app/public/diff/gabsl_measurements_19245.diff
[CMD] [2019-12-23 02:20:15] tail -n +1 /app/public/converted_csv/gabsl_measurements_19245.csv >> /app/public/diff/gabsl_measurements_19245.diff
[CMD] [2019-12-23 02:20:15] echo "." >> /app/public/diff/gabsl_measurements_19245.diff
[STOP] [2019-12-23 02:20:15] calculate_delta
[START] [2019-12-23 02:20:15] parse_diff_and_store
[INFO] [2019-12-23 02:20:15] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 02:20:15] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 02:20:20] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 02:20:21] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 02:20:58] Storing 2 References
[INFO] [2019-12-23 02:20:58] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 02:20:58] Average Time: 0.0
[INFO] [2019-12-23 02:20:58] Total Time: 1s
[INFO] [2019-12-23 02:20:58] Storing 11384 ScientificNames
[INFO] [2019-12-23 02:20:58] Processing group of 11384 in 12 groups of 1000
[INFO] [2019-12-23 02:21:03] Average Time: 0.412
[INFO] [2019-12-23 02:21:03] Total Time: 5s
[INFO] [2019-12-23 02:21:03] last 3 / first 3: 0.59
[INFO] [2019-12-23 02:21:03] Std.Dev: 0.10954451150103323; Max: 0.56
[INFO] [2019-12-23 02:21:03] Storing 11384 Nodes
[INFO] [2019-12-23 02:21:03] Processing group of 11384 in 12 groups of 1000
[INFO] [2019-12-23 02:21:07] Average Time: 0.314
[INFO] [2019-12-23 02:21:07] Total Time: 4s
[INFO] [2019-12-23 02:21:07] last 3 / first 3: 0.8
[INFO] [2019-12-23 02:21:07] Std.Dev: 0.06324555320336758; Max: 0.37
[INFO] [2019-12-23 02:21:07] Storing 6412 Occurrences
[INFO] [2019-12-23 02:21:07] Processing group of 6412 in 7 groups of 1000
[INFO] [2019-12-23 02:21:08] Average Time: 0.107
[INFO] [2019-12-23 02:21:08] Total Time: 1s
[INFO] [2019-12-23 02:21:08] last 3 / first 3: 0.76
[INFO] [2019-12-23 02:21:08] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-12-23 02:21:08] Storing 12824 TraitsReferences
[INFO] [2019-12-23 02:21:08] Processing group of 12824 in 13 groups of 1000
[INFO] [2019-12-23 02:21:09] Average Time: 0.088
[INFO] [2019-12-23 02:21:09] Total Time: 2s
[INFO] [2019-12-23 02:21:09] last 3 / first 3: 0.59
[INFO] [2019-12-23 02:21:09] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-12-23 02:21:09] Storing 12824 Traits
[INFO] [2019-12-23 02:21:09] Processing group of 12824 in 13 groups of 1000
[INFO] [2019-12-23 02:21:13] Average Time: 0.341
[INFO] [2019-12-23 02:21:13] Total Time: 5s
[INFO] [2019-12-23 02:21:13] last 3 / first 3: 0.82
[INFO] [2019-12-23 02:21:13] Std.Dev: 0.03162277660168379; Max: 0.44
[INFO] [2019-12-23 02:21:13] Storing 12781 MetaTraits
[INFO] [2019-12-23 02:21:13] Processing group of 12781 in 13 groups of 1000
[INFO] [2019-12-23 02:21:15] Average Time: 0.131
[INFO] [2019-12-23 02:21:15] Total Time: 2s
[INFO] [2019-12-23 02:21:15] last 3 / first 3: 0.85
[INFO] [2019-12-23 02:21:15] Std.Dev: 0.0; Max: 0.16
[STOP] [2019-12-23 02:21:15] parse_diff_and_store
[START] [2019-12-23 02:21:15] resolve_keys
[INFO] [2019-12-23 02:22:02] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 02:22:06] traits to occurrences...
[INFO] [2019-12-23 02:22:11] traits to nodes (through occurrences)...
[INFO] [2019-12-23 02:22:11] Traits to sex term...
[INFO] [2019-12-23 02:22:15] Traits to lifestage term...
[INFO] [2019-12-23 02:22:20] MetaTraits to traits...
[INFO] [2019-12-23 02:22:21] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 02:22:23] Assocs to occurrences...
[INFO] [2019-12-23 02:22:23] Assocs to nodes...
[INFO] [2019-12-23 02:22:23] Assoc to sex term...
[INFO] [2019-12-23 02:22:23] Assoc to lifestage term...
[STOP] [2019-12-23 02:22:23] resolve_keys
[START] [2019-12-23 02:22:23] hold_for_later_1
[STOP] [2019-12-23 02:22:23] hold_for_later_1
[START] [2019-12-23 02:22:23] hold_for_later_2
[STOP] [2019-12-23 02:22:23] hold_for_later_2
[START] [2019-12-23 02:22:23] resolve_missing_parents
[STOP] [2019-12-23 02:22:43] resolve_missing_parents
[START] [2019-12-23 02:22:43] rebuild_nodes
[START] [2019-12-23 02:22:43] Flattener#flatten
[START] [2019-12-23 02:22:43] Flattener#study_resource
[START] [2019-12-23 02:22:43] Flattener#build_ancestry
[STOP] [2019-12-23 02:22:44] Flattener#build_ancestry
[INFO] [2019-12-23 02:22:44] 11384 ancestry keys
[START] [2019-12-23 02:22:44] build_node_ancestors
[INFO] [2019-12-23 02:22:44] old ancestors deleted.
[STOP] [2019-12-23 02:22:49] build_node_ancestors
[START] [2019-12-23 02:22:53] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 02:22:55] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 02:22:55] Flattener#flatten
[STOP] [2019-12-23 02:22:55] rebuild_nodes
[START] [2019-12-23 02:22:55] resolve_missing_media_owners
[STOP] [2019-12-23 02:22:55] resolve_missing_media_owners
[START] [2019-12-23 02:22:55] sanitize_media_verbatims
[STOP] [2019-12-23 02:22:55] sanitize_media_verbatims
[START] [2019-12-23 02:22:55] queue_downloads
[STOP] [2019-12-23 02:22:55] queue_downloads
[START] [2019-12-23 02:22:55] parse_names
[WARN] [2019-12-23 02:22:55] I see 11384 names which still need to be parsed.
[STOP] [2019-12-23 02:23:05] parse_names
[START] [2019-12-23 02:23:05] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 02:23:05] denormalize_canonical_names_to_nodes
[START] [2019-12-23 02:23:05] match_nodes
[START] [2019-12-23 02:23:05] map_all_nodes_to_pages
[STOP] [2019-12-23 03:12:32] map_all_nodes_to_pages
[INFO] [2019-12-23 03:12:32] 746 Unmatched nodes (of 11384)! That's too many to output. First 10: Limicola (#61888055); Limicola falcinellus (#61888054); Philomachus (#61888172); Philomachus pugnax (#61888171); Egretta intermedia (#61881693); Anas rhynchotis (#61879730); Puffinus tenuirostris (#61879571); Puffinus carneipes (#61879930); Puffinus griseus (#61880213); Puffinus pacificus (#61884523)
[START] [2019-12-23 03:12:32] update_nodes
[STOP] [2019-12-23 03:12:36] update_nodes
[STOP] [2019-12-23 03:12:36] match_nodes
[START] [2019-12-23 03:12:36] reindex_search
[STOP] [2019-12-23 03:13:03] reindex_search
[START] [2019-12-23 03:13:03] normalize_units
[STOP] [2019-12-23 03:13:03] normalize_units
[START] [2019-12-23 03:13:03] calculate_statistics
[STOP] [2019-12-23 03:13:03] calculate_statistics
[START] [2019-12-23 03:13:03] complete_harvest_instance
[START] [2019-12-23 03:13:03] overall_tsv_creation
[INFO] [2019-12-23 03:13:03] Processing group of 11384 in 2 batches of 10000
[INFO] [2019-12-23 03:14:33] 5510 Traits (unfiltered)...
[INFO] [2019-12-23 03:14:47] 5510 Traits (filtered)...
[INFO] [2019-12-23 03:14:47] 0 Associations (filtered)...
[INFO] [2019-12-23 03:15:39] 27509 metadata added.
[INFO] [2019-12-23 03:15:39] 0 metadata added.
[INFO] [2019-12-23 03:16:33] 902 Traits (unfiltered)...
[INFO] [2019-12-23 03:16:46] 902 Traits (filtered)...
[INFO] [2019-12-23 03:16:46] 0 Associations (filtered)...
[INFO] [2019-12-23 03:17:26] 4508 metadata added.
[INFO] [2019-12-23 03:17:26] 0 metadata added.
[INFO] [2019-12-23 03:17:26] Average Time: 104.53
[INFO] [2019-12-23 03:17:26] Total Time: 4m23s
[STOP] [2019-12-23 03:17:26] overall_tsv_creation
[INFO] [2019-12-23 03:17:26] Done. Check your files:
[INFO] [2019-12-23 03:17:26] (11384 lines) /app/public/data/gabsl/publish_nodes.tsv
[INFO] [2019-12-23 03:17:26] (59325 lines) /app/public/data/gabsl/publish_node_ancestors.tsv
[INFO] [2019-12-23 03:17:26] (11384 lines) /app/public/data/gabsl/publish_scientific_names.tsv
[INFO] [2019-12-23 03:17:26] (6413 lines) /app/public/data/gabsl/publish_traits.tsv
[INFO] [2019-12-23 03:17:26] (32018 lines) /app/public/data/gabsl/publish_metadata.tsv
[STOP] [2019-12-23 03:17:26] complete_harvest_instance
[START] [2019-12-23 03:17:26] completed
[STOP] [2019-12-23 03:17:26] completed
[STOP] [2019-12-23 03:17:26] logged process, took 3434.3
Latest Process

23 Dec 02:20 EXITED currently processing 0