Harvest for Equatorial Guinea Species List Created 12 Oct 17:23

Stage: completed
Fetched: 12 Oct 17:23
Validated: 12 Oct 17:23
Deltas Created 12 Oct 17:23
Units Normalized: 12 Oct 17:34
Ancestry Built: 12 Oct 17:25
Nodes Matched: 12 Oct 17:33
Names Parsed: 12 Oct 17:25
New Models Stored: 12 Oct 17:24
Indexed: 12 Oct 17:34
Completed: 12 Oct 17:36
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-12 17:23:53 -0400 by logger.rb/56815
[START] [2019-10-12 17:23:53] logged process
[START] [2019-10-12 17:23:53] create_harvest_instance
[STOP] [2019-10-12 17:23:53] create_harvest_instance
[START] [2019-10-12 17:23:53] fetch_files
[STOP] [2019-10-12 17:23:53] fetch_files
[START] [2019-10-12 17:23:53] validate_each_file
[STOP] [2019-10-12 17:23:54] validate_each_file
[START] [2019-10-12 17:23:54] convert_to_csv
[CMD] [2019-10-12 17:23:54] /usr/bin/sort /app/public/converted_csv/equatorial_guine_refs_15667.csv > /app/public/converted_csv/equatorial_guine_refs_15667.csv_sorted
[CMD] [2019-10-12 17:23:54] /usr/bin/sort /app/public/converted_csv/equatorial_guine_nodes_15668.csv > /app/public/converted_csv/equatorial_guine_nodes_15668.csv_sorted
[CMD] [2019-10-12 17:23:54] /usr/bin/sort /app/public/converted_csv/equatorial_guine_occurrences_15669.csv > /app/public/converted_csv/equatorial_guine_occurrences_15669.csv_sorted
[CMD] [2019-10-12 17:23:55] /usr/bin/sort /app/public/converted_csv/equatorial_guine_measurements_15670.csv > /app/public/converted_csv/equatorial_guine_measurements_15670.csv_sorted
[STOP] [2019-10-12 17:23:55] convert_to_csv
[START] [2019-10-12 17:23:55] calculate_delta
[CMD] [2019-10-12 17:23:55] echo "0a" > /app/public/diff/equatorial_guine_refs_15667.diff
[CMD] [2019-10-12 17:23:55] tail -n +1 /app/public/converted_csv/equatorial_guine_refs_15667.csv >> /app/public/diff/equatorial_guine_refs_15667.diff
[CMD] [2019-10-12 17:23:55] echo "." >> /app/public/diff/equatorial_guine_refs_15667.diff
[CMD] [2019-10-12 17:23:55] echo "0a" > /app/public/diff/equatorial_guine_nodes_15668.diff
[CMD] [2019-10-12 17:23:55] tail -n +1 /app/public/converted_csv/equatorial_guine_nodes_15668.csv >> /app/public/diff/equatorial_guine_nodes_15668.diff
[CMD] [2019-10-12 17:23:55] echo "." >> /app/public/diff/equatorial_guine_nodes_15668.diff
[CMD] [2019-10-12 17:23:55] echo "0a" > /app/public/diff/equatorial_guine_occurrences_15669.diff
[CMD] [2019-10-12 17:23:55] tail -n +1 /app/public/converted_csv/equatorial_guine_occurrences_15669.csv >> /app/public/diff/equatorial_guine_occurrences_15669.diff
[CMD] [2019-10-12 17:23:55] echo "." >> /app/public/diff/equatorial_guine_occurrences_15669.diff
[CMD] [2019-10-12 17:23:56] echo "0a" > /app/public/diff/equatorial_guine_measurements_15670.diff
[CMD] [2019-10-12 17:23:56] tail -n +1 /app/public/converted_csv/equatorial_guine_measurements_15670.csv >> /app/public/diff/equatorial_guine_measurements_15670.diff
[CMD] [2019-10-12 17:23:56] echo "." >> /app/public/diff/equatorial_guine_measurements_15670.diff
[STOP] [2019-10-12 17:23:56] calculate_delta
[START] [2019-10-12 17:23:56] parse_diff_and_store
[INFO] [2019-10-12 17:23:56] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 17:23:56] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 17:23:59] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 17:24:00] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 17:24:26] Storing 2 References
[INFO] [2019-10-12 17:24:26] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 17:24:26] Average Time: 0.0
[INFO] [2019-10-12 17:24:26] Total Time: 1s
[INFO] [2019-10-12 17:24:26] Storing 7020 ScientificNames
[INFO] [2019-10-12 17:24:26] Processing group of 7020 in 8 groups of 1000
[INFO] [2019-10-12 17:24:28] Average Time: 0.309
[INFO] [2019-10-12 17:24:28] Total Time: 3s
[INFO] [2019-10-12 17:24:28] last 3 / first 3: 0.56
[INFO] [2019-10-12 17:24:28] Std.Dev: 0.12649110640673517; Max: 0.45
[INFO] [2019-10-12 17:24:28] Storing 7020 Nodes
[INFO] [2019-10-12 17:24:28] Processing group of 7020 in 8 groups of 1000
[INFO] [2019-10-12 17:24:30] Average Time: 0.262
[INFO] [2019-10-12 17:24:30] Total Time: 3s
[INFO] [2019-10-12 17:24:30] last 3 / first 3: 0.6
[INFO] [2019-10-12 17:24:30] Std.Dev: 0.10954451150103323; Max: 0.39
[INFO] [2019-10-12 17:24:30] Storing 4395 Occurrences
[INFO] [2019-10-12 17:24:30] Processing group of 4395 in 5 groups of 1000
[INFO] [2019-10-12 17:24:31] Average Time: 0.09
[INFO] [2019-10-12 17:24:31] Total Time: 1s
[INFO] [2019-10-12 17:24:31] Storing 8790 TraitsReferences
[INFO] [2019-10-12 17:24:31] Processing group of 8790 in 9 groups of 1000
[INFO] [2019-10-12 17:24:31] Average Time: 0.067
[INFO] [2019-10-12 17:24:31] Total Time: 1s
[INFO] [2019-10-12 17:24:31] last 3 / first 3: 0.68
[INFO] [2019-10-12 17:24:31] Std.Dev: 0.03162277660168379; Max: 0.13
[INFO] [2019-10-12 17:24:31] Storing 8790 Traits
[INFO] [2019-10-12 17:24:31] Processing group of 8790 in 9 groups of 1000
[INFO] [2019-10-12 17:24:34] Average Time: 0.307
[INFO] [2019-10-12 17:24:34] Total Time: 3s
[INFO] [2019-10-12 17:24:34] last 3 / first 3: 0.83
[INFO] [2019-10-12 17:24:34] Std.Dev: 0.05477225575051661; Max: 0.45
[INFO] [2019-10-12 17:24:34] Storing 8780 MetaTraits
[INFO] [2019-10-12 17:24:34] Processing group of 8780 in 9 groups of 1000
[INFO] [2019-10-12 17:24:35] Average Time: 0.127
[INFO] [2019-10-12 17:24:35] Total Time: 2s
[INFO] [2019-10-12 17:24:35] last 3 / first 3: 0.81
[INFO] [2019-10-12 17:24:35] Std.Dev: 0.0; Max: 0.17
[STOP] [2019-10-12 17:24:35] parse_diff_and_store
[START] [2019-10-12 17:24:35] resolve_keys
[INFO] [2019-10-12 17:25:05] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 17:25:08] traits to occurrences...
[INFO] [2019-10-12 17:25:10] traits to nodes (through occurrences)...
[INFO] [2019-10-12 17:25:10] Traits to sex term...
[INFO] [2019-10-12 17:25:11] Traits to lifestage term...
[INFO] [2019-10-12 17:25:13] MetaTraits to traits...
[INFO] [2019-10-12 17:25:14] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 17:25:15] Assocs to occurrences...
[INFO] [2019-10-12 17:25:15] Assocs to nodes...
[INFO] [2019-10-12 17:25:15] Assoc to sex term...
[INFO] [2019-10-12 17:25:15] Assoc to lifestage term...
[STOP] [2019-10-12 17:25:15] resolve_keys
[START] [2019-10-12 17:25:15] hold_for_later_1
[STOP] [2019-10-12 17:25:15] hold_for_later_1
[START] [2019-10-12 17:25:15] hold_for_later_2
[STOP] [2019-10-12 17:25:15] hold_for_later_2
[START] [2019-10-12 17:25:15] resolve_missing_parents
[STOP] [2019-10-12 17:25:29] resolve_missing_parents
[START] [2019-10-12 17:25:29] rebuild_nodes
[START] [2019-10-12 17:25:29] Flattener#flatten
[START] [2019-10-12 17:25:29] Flattener#study_resource
[START] [2019-10-12 17:25:29] Flattener#build_ancestry
[STOP] [2019-10-12 17:25:29] Flattener#build_ancestry
[INFO] [2019-10-12 17:25:29] 7020 ancestry keys
[START] [2019-10-12 17:25:29] build_node_ancestors
[INFO] [2019-10-12 17:25:29] old ancestors deleted.
[STOP] [2019-10-12 17:25:32] build_node_ancestors
[START] [2019-10-12 17:25:35] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 17:25:36] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 17:25:36] Flattener#flatten
[STOP] [2019-10-12 17:25:36] rebuild_nodes
[START] [2019-10-12 17:25:36] resolve_missing_media_owners
[STOP] [2019-10-12 17:25:36] resolve_missing_media_owners
[START] [2019-10-12 17:25:36] sanitize_media_verbatims
[STOP] [2019-10-12 17:25:36] sanitize_media_verbatims
[START] [2019-10-12 17:25:36] queue_downloads
[STOP] [2019-10-12 17:25:36] queue_downloads
[START] [2019-10-12 17:25:36] parse_names
[WARN] [2019-10-12 17:25:36] I see 7020 names which still need to be parsed.
[STOP] [2019-10-12 17:25:42] parse_names
[START] [2019-10-12 17:25:42] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 17:25:42] denormalize_canonical_names_to_nodes
[START] [2019-10-12 17:25:42] match_nodes
[START] [2019-10-12 17:25:42] map_all_nodes_to_pages
[STOP] [2019-10-12 17:33:56] map_all_nodes_to_pages
[INFO] [2019-10-12 17:33:56] 231 Unmatched nodes (of 7020)! That's too many to output. First 10: Magnoliophyta (#49547785); Magnoliopsida (#49547784); Laccodiscus spinuloso-dentatus (#49551829); Fagara (#49551075); Citrus sinensis (#49551689); Oriciopsis (#49554075); Sclerocroton cornutum (#49549484); Croton silvaticus (#49550870); Astraea lobatus (#49553711); Garcinia quadriferia (#49553166)
[START] [2019-10-12 17:33:56] update_nodes
[STOP] [2019-10-12 17:33:59] update_nodes
[STOP] [2019-10-12 17:33:59] match_nodes
[START] [2019-10-12 17:33:59] reindex_search
[STOP] [2019-10-12 17:34:19] reindex_search
[START] [2019-10-12 17:34:19] normalize_units
[STOP] [2019-10-12 17:34:19] normalize_units
[START] [2019-10-12 17:34:19] calculate_statistics
[STOP] [2019-10-12 17:34:19] calculate_statistics
[START] [2019-10-12 17:34:19] complete_harvest_instance
[START] [2019-10-12 17:34:19] overall_tsv_creation
[INFO] [2019-10-12 17:34:19] Processing group of 7020 in 1 batches of 10000
[INFO] [2019-10-12 17:35:35] 4395 Traits (unfiltered)...
[INFO] [2019-10-12 17:35:49] 4395 Traits (filtered)...
[INFO] [2019-10-12 17:35:49] 0 Associations (filtered)...
[INFO] [2019-10-12 17:36:35] 21965 metadata added.
[INFO] [2019-10-12 17:36:35] 0 metadata added.
[INFO] [2019-10-12 17:36:35] Average Time: 110.0
[INFO] [2019-10-12 17:36:35] Total Time: 2m16s
[STOP] [2019-10-12 17:36:35] overall_tsv_creation
[INFO] [2019-10-12 17:36:35] Done. Check your files:
[INFO] [2019-10-12 17:36:35] (7020 lines) /app/public/data/equatorial_guine/publish_nodes.tsv
[INFO] [2019-10-12 17:36:35] (38237 lines) /app/public/data/equatorial_guine/publish_node_ancestors.tsv
[INFO] [2019-10-12 17:36:35] (7020 lines) /app/public/data/equatorial_guine/publish_scientific_names.tsv
[INFO] [2019-10-12 17:36:35] (4396 lines) /app/public/data/equatorial_guine/publish_traits.tsv
[INFO] [2019-10-12 17:36:35] (21966 lines) /app/public/data/equatorial_guine/publish_metadata.tsv
[STOP] [2019-10-12 17:36:35] complete_harvest_instance
[START] [2019-10-12 17:36:35] completed
[STOP] [2019-10-12 17:36:35] completed
[STOP] [2019-10-12 17:36:35] logged process, took 762.6
Latest Process

12 Oct 17:23 EXITED currently processing 0