Harvest for Guyana Species List Created 13 Oct 10:03

Stage: completed
Fetched: 13 Oct 10:03
Validated: 13 Oct 10:03
Deltas Created 13 Oct 10:03
Units Normalized: 13 Oct 10:23
Ancestry Built: 13 Oct 10:06
Nodes Matched: 13 Oct 10:22
Names Parsed: 13 Oct 10:07
New Models Stored: 13 Oct 10:04
Indexed: 13 Oct 10:23
Completed: 13 Oct 10:27
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-13 10:03:05 -0400 by logger.rb/56815
[START] [2019-10-13 10:03:05] logged process
[START] [2019-10-13 10:03:05] create_harvest_instance
[STOP] [2019-10-13 10:03:06] create_harvest_instance
[START] [2019-10-13 10:03:06] fetch_files
[STOP] [2019-10-13 10:03:06] fetch_files
[START] [2019-10-13 10:03:06] validate_each_file
[STOP] [2019-10-13 10:03:08] validate_each_file
[START] [2019-10-13 10:03:08] convert_to_csv
[CMD] [2019-10-13 10:03:08] /usr/bin/sort /app/public/converted_csv/guyana_sp_list_refs_16067.csv > /app/public/converted_csv/guyana_sp_list_refs_16067.csv_sorted
[CMD] [2019-10-13 10:03:08] /usr/bin/sort /app/public/converted_csv/guyana_sp_list_nodes_16068.csv > /app/public/converted_csv/guyana_sp_list_nodes_16068.csv_sorted
[CMD] [2019-10-13 10:03:08] /usr/bin/sort /app/public/converted_csv/guyana_sp_list_occurrences_16069.csv > /app/public/converted_csv/guyana_sp_list_occurrences_16069.csv_sorted
[CMD] [2019-10-13 10:03:08] /usr/bin/sort /app/public/converted_csv/guyana_sp_list_measurements_16070.csv > /app/public/converted_csv/guyana_sp_list_measurements_16070.csv_sorted
[STOP] [2019-10-13 10:03:09] convert_to_csv
[START] [2019-10-13 10:03:09] calculate_delta
[CMD] [2019-10-13 10:03:09] echo "0a" > /app/public/diff/guyana_sp_list_refs_16067.diff
[CMD] [2019-10-13 10:03:09] tail -n +1 /app/public/converted_csv/guyana_sp_list_refs_16067.csv >> /app/public/diff/guyana_sp_list_refs_16067.diff
[CMD] [2019-10-13 10:03:09] echo "." >> /app/public/diff/guyana_sp_list_refs_16067.diff
[CMD] [2019-10-13 10:03:09] echo "0a" > /app/public/diff/guyana_sp_list_nodes_16068.diff
[CMD] [2019-10-13 10:03:09] tail -n +1 /app/public/converted_csv/guyana_sp_list_nodes_16068.csv >> /app/public/diff/guyana_sp_list_nodes_16068.diff
[CMD] [2019-10-13 10:03:09] echo "." >> /app/public/diff/guyana_sp_list_nodes_16068.diff
[CMD] [2019-10-13 10:03:09] echo "0a" > /app/public/diff/guyana_sp_list_occurrences_16069.diff
[CMD] [2019-10-13 10:03:09] tail -n +1 /app/public/converted_csv/guyana_sp_list_occurrences_16069.csv >> /app/public/diff/guyana_sp_list_occurrences_16069.diff
[CMD] [2019-10-13 10:03:09] echo "." >> /app/public/diff/guyana_sp_list_occurrences_16069.diff
[CMD] [2019-10-13 10:03:09] echo "0a" > /app/public/diff/guyana_sp_list_measurements_16070.diff
[CMD] [2019-10-13 10:03:09] tail -n +1 /app/public/converted_csv/guyana_sp_list_measurements_16070.csv >> /app/public/diff/guyana_sp_list_measurements_16070.diff
[CMD] [2019-10-13 10:03:10] echo "." >> /app/public/diff/guyana_sp_list_measurements_16070.diff
[STOP] [2019-10-13 10:03:10] calculate_delta
[START] [2019-10-13 10:03:10] parse_diff_and_store
[INFO] [2019-10-13 10:03:10] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 10:03:10] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 10:03:16] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 10:03:17] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 10:04:22] Storing 2 References
[INFO] [2019-10-13 10:04:22] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 10:04:22] Average Time: 0.0
[INFO] [2019-10-13 10:04:22] Total Time: 1s
[INFO] [2019-10-13 10:04:22] Storing 15420 ScientificNames
[INFO] [2019-10-13 10:04:22] Processing group of 15420 in 16 groups of 1000
[INFO] [2019-10-13 10:04:28] Average Time: 0.354
[INFO] [2019-10-13 10:04:28] Total Time: 6s
[INFO] [2019-10-13 10:04:28] last 3 / first 3: 0.75
[INFO] [2019-10-13 10:04:28] Std.Dev: 0.05477225575051661; Max: 0.42
[INFO] [2019-10-13 10:04:28] Storing 15420 Nodes
[INFO] [2019-10-13 10:04:28] Processing group of 15420 in 16 groups of 1000
[INFO] [2019-10-13 10:04:34] Average Time: 0.339
[INFO] [2019-10-13 10:04:34] Total Time: 6s
[INFO] [2019-10-13 10:04:34] last 3 / first 3: 1.37
[INFO] [2019-10-13 10:04:34] Std.Dev: 0.13784048752090222; Max: 0.78
[INFO] [2019-10-13 10:04:34] Storing 11086 Occurrences
[INFO] [2019-10-13 10:04:34] Processing group of 11086 in 12 groups of 1000
[INFO] [2019-10-13 10:04:35] Average Time: 0.098
[INFO] [2019-10-13 10:04:35] Total Time: 2s
[INFO] [2019-10-13 10:04:35] last 3 / first 3: 0.64
[INFO] [2019-10-13 10:04:35] Std.Dev: 0.03162277660168379; Max: 0.13
[INFO] [2019-10-13 10:04:35] Storing 22430 TraitsReferences
[INFO] [2019-10-13 10:04:35] Processing group of 22430 in 23 groups of 1000
[INFO] [2019-10-13 10:04:37] Average Time: 0.072
[INFO] [2019-10-13 10:04:37] Total Time: 2s
[INFO] [2019-10-13 10:04:37] last 3 / first 3: 0.57
[INFO] [2019-10-13 10:04:37] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-10-13 10:04:37] Storing 22429 Traits
[INFO] [2019-10-13 10:04:37] Processing group of 22429 in 23 groups of 1000
[INFO] [2019-10-13 10:04:44] Average Time: 0.313
[INFO] [2019-10-13 10:04:44] Total Time: 8s
[INFO] [2019-10-13 10:04:44] last 3 / first 3: 0.76
[INFO] [2019-10-13 10:04:44] Std.Dev: 0.05477225575051661; Max: 0.43
[INFO] [2019-10-13 10:04:44] Storing 22420 MetaTraits
[INFO] [2019-10-13 10:04:44] Processing group of 22420 in 23 groups of 1000
[INFO] [2019-10-13 10:04:47] Average Time: 0.132
[INFO] [2019-10-13 10:04:47] Total Time: 4s
[INFO] [2019-10-13 10:04:47] last 3 / first 3: 0.74
[INFO] [2019-10-13 10:04:47] Std.Dev: 0.03162277660168379; Max: 0.18
[STOP] [2019-10-13 10:04:47] parse_diff_and_store
[START] [2019-10-13 10:04:47] resolve_keys
[INFO] [2019-10-13 10:05:48] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 10:05:53] traits to occurrences...
[INFO] [2019-10-13 10:05:57] traits to nodes (through occurrences)...
[INFO] [2019-10-13 10:05:57] Traits to sex term...
[INFO] [2019-10-13 10:06:01] Traits to lifestage term...
[INFO] [2019-10-13 10:06:04] MetaTraits to traits...
[INFO] [2019-10-13 10:06:06] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 10:06:09] Assocs to occurrences...
[INFO] [2019-10-13 10:06:09] Assocs to nodes...
[INFO] [2019-10-13 10:06:09] Assoc to sex term...
[INFO] [2019-10-13 10:06:09] Assoc to lifestage term...
[STOP] [2019-10-13 10:06:09] resolve_keys
[START] [2019-10-13 10:06:09] hold_for_later_1
[STOP] [2019-10-13 10:06:09] hold_for_later_1
[START] [2019-10-13 10:06:09] hold_for_later_2
[STOP] [2019-10-13 10:06:09] hold_for_later_2
[START] [2019-10-13 10:06:09] resolve_missing_parents
[STOP] [2019-10-13 10:06:43] resolve_missing_parents
[START] [2019-10-13 10:06:43] rebuild_nodes
[START] [2019-10-13 10:06:43] Flattener#flatten
[START] [2019-10-13 10:06:43] Flattener#study_resource
[START] [2019-10-13 10:06:43] Flattener#build_ancestry
[STOP] [2019-10-13 10:06:45] Flattener#build_ancestry
[INFO] [2019-10-13 10:06:45] 15420 ancestry keys
[START] [2019-10-13 10:06:45] build_node_ancestors
[INFO] [2019-10-13 10:06:45] old ancestors deleted.
[STOP] [2019-10-13 10:06:48] build_node_ancestors
[START] [2019-10-13 10:06:51] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 10:06:52] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 10:06:52] Flattener#flatten
[STOP] [2019-10-13 10:06:52] rebuild_nodes
[START] [2019-10-13 10:06:52] resolve_missing_media_owners
[STOP] [2019-10-13 10:06:52] resolve_missing_media_owners
[START] [2019-10-13 10:06:52] sanitize_media_verbatims
[STOP] [2019-10-13 10:06:52] sanitize_media_verbatims
[START] [2019-10-13 10:06:52] queue_downloads
[STOP] [2019-10-13 10:06:52] queue_downloads
[START] [2019-10-13 10:06:52] parse_names
[WARN] [2019-10-13 10:06:52] I see 15420 names which still need to be parsed.
[STOP] [2019-10-13 10:07:04] parse_names
[START] [2019-10-13 10:07:04] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 10:07:04] denormalize_canonical_names_to_nodes
[START] [2019-10-13 10:07:04] match_nodes
[START] [2019-10-13 10:07:04] map_all_nodes_to_pages
[STOP] [2019-10-13 10:22:15] map_all_nodes_to_pages
[INFO] [2019-10-13 10:22:15] 941 Unmatched nodes (of 15420)! That's too many to output. First 10: Artibeus gnoma (#50061804); Dermanura cinereus (#50046474); Dermanura glaucus (#50046747); Dermanura gnomus (#50047226); Lophostoma silvicola (#50047400); Pitangus lictor (#50046834); Conopias parva (#50048127); Contopus borealis (#50057086); Corythopis torquata (#50055376); Phylloscartes chapmani (#50050567)
[START] [2019-10-13 10:22:15] update_nodes
[STOP] [2019-10-13 10:22:20] update_nodes
[STOP] [2019-10-13 10:22:20] match_nodes
[START] [2019-10-13 10:22:20] reindex_search
[STOP] [2019-10-13 10:23:04] reindex_search
[START] [2019-10-13 10:23:04] normalize_units
[STOP] [2019-10-13 10:23:04] normalize_units
[START] [2019-10-13 10:23:04] calculate_statistics
[STOP] [2019-10-13 10:23:04] calculate_statistics
[START] [2019-10-13 10:23:04] complete_harvest_instance
[START] [2019-10-13 10:23:04] overall_tsv_creation
[INFO] [2019-10-13 10:23:04] Processing group of 15420 in 2 batches of 10000
[INFO] [2019-10-13 10:24:32] 6746 Traits (unfiltered)...
[INFO] [2019-10-13 10:24:46] 6746 Traits (filtered)...
[INFO] [2019-10-13 10:24:46] 0 Associations (filtered)...
[INFO] [2019-10-13 10:25:38] 33726 metadata added.
[INFO] [2019-10-13 10:25:38] 0 metadata added.
[INFO] [2019-10-13 10:26:46] 4340 Traits (unfiltered)...
[INFO] [2019-10-13 10:27:00] 4340 Traits (filtered)...
[INFO] [2019-10-13 10:27:00] 0 Associations (filtered)...
[INFO] [2019-10-13 10:27:46] 21694 metadata added.
[INFO] [2019-10-13 10:27:46] 0 metadata added.
[INFO] [2019-10-13 10:27:46] Average Time: 116.565
[INFO] [2019-10-13 10:27:46] Total Time: 4m43s
[STOP] [2019-10-13 10:27:46] overall_tsv_creation
[INFO] [2019-10-13 10:27:46] Done. Check your files:
[INFO] [2019-10-13 10:27:47] (15420 lines) /app/public/data/guyana_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 10:27:47] (40693 lines) /app/public/data/guyana_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 10:27:47] (15420 lines) /app/public/data/guyana_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 10:27:47] (11087 lines) /app/public/data/guyana_sp_list/publish_traits.tsv
[INFO] [2019-10-13 10:27:47] (55421 lines) /app/public/data/guyana_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 10:27:47] complete_harvest_instance
[START] [2019-10-13 10:27:47] completed
[STOP] [2019-10-13 10:27:47] completed
[STOP] [2019-10-13 10:27:47] logged process, took 1482.08
Latest Process

13 Oct 10:03 EXITED currently processing 0