Harvest for Kissling et al, 2014 Created 12 Jul 14:39

Stage: completed
Fetched: 12 Jul 14:39
Validated: 12 Jul 14:39
Deltas Created 12 Jul 14:39
Units Normalized: 12 Jul 14:45
Ancestry Built: 12 Jul 14:40
Nodes Matched: 12 Jul 14:45
Names Parsed: 12 Jul 14:40
New Models Stored: 12 Jul 14:40
Indexed: 12 Jul 14:45
Completed: 12 Jul 14:48
Time to Harvest: less than a minute

Harvesting Log

(136 lines)
# Logfile created on 2019-07-12 14:39:24 -0400 by logger.rb/56815
[START] [2019-07-12 14:39:24] logged process
[START] [2019-07-12 14:39:24] create_harvest_instance
[STOP] [2019-07-12 14:39:25] create_harvest_instance
[START] [2019-07-12 14:39:25] fetch_files
[STOP] [2019-07-12 14:39:25] fetch_files
[START] [2019-07-12 14:39:25] validate_each_file
[STOP] [2019-07-12 14:39:26] validate_each_file
[START] [2019-07-12 14:39:26] convert_to_csv
[CMD] [2019-07-12 14:39:26] /usr/bin/sort /app/public/converted_csv/mam_diet_nodes_14201.csv > /app/public/converted_csv/mam_diet_nodes_14201.csv_sorted
[CMD] [2019-07-12 14:39:26] /usr/bin/sort /app/public/converted_csv/mam_diet_occurrences_14202.csv > /app/public/converted_csv/mam_diet_occurrences_14202.csv_sorted
[CMD] [2019-07-12 14:39:26] /usr/bin/sort /app/public/converted_csv/mam_diet_measurements_14203.csv > /app/public/converted_csv/mam_diet_measurements_14203.csv_sorted
[STOP] [2019-07-12 14:39:26] convert_to_csv
[START] [2019-07-12 14:39:26] calculate_delta
[CMD] [2019-07-12 14:39:26] echo "0a" > /app/public/diff/mam_diet_nodes_14201.diff
[CMD] [2019-07-12 14:39:26] tail -n +1 /app/public/converted_csv/mam_diet_nodes_14201.csv >> /app/public/diff/mam_diet_nodes_14201.diff
[CMD] [2019-07-12 14:39:26] echo "." >> /app/public/diff/mam_diet_nodes_14201.diff
[CMD] [2019-07-12 14:39:26] echo "0a" > /app/public/diff/mam_diet_occurrences_14202.diff
[CMD] [2019-07-12 14:39:26] tail -n +1 /app/public/converted_csv/mam_diet_occurrences_14202.csv >> /app/public/diff/mam_diet_occurrences_14202.diff
[CMD] [2019-07-12 14:39:26] echo "." >> /app/public/diff/mam_diet_occurrences_14202.diff
[CMD] [2019-07-12 14:39:27] echo "0a" > /app/public/diff/mam_diet_measurements_14203.diff
[CMD] [2019-07-12 14:39:27] tail -n +1 /app/public/converted_csv/mam_diet_measurements_14203.csv >> /app/public/diff/mam_diet_measurements_14203.diff
[CMD] [2019-07-12 14:39:27] echo "." >> /app/public/diff/mam_diet_measurements_14203.diff
[STOP] [2019-07-12 14:39:27] calculate_delta
[START] [2019-07-12 14:39:27] parse_diff_and_store
[INFO] [2019-07-12 14:39:27] Loading nodes diff file into memory (true lines)...
[INFO] [2019-07-12 14:39:30] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-07-12 14:39:31] Loading measurements diff file into memory (true lines)...
[INFO] [2019-07-12 14:39:58] Storing 6705 ScientificNames
[INFO] [2019-07-12 14:39:58] Processing group of 6705 in 7 groups of 1000
[INFO] [2019-07-12 14:40:00] Average Time: 0.354
[INFO] [2019-07-12 14:40:00] Total Time: 3s
[INFO] [2019-07-12 14:40:00] last 3 / first 3: 0.84
[INFO] [2019-07-12 14:40:00] Std.Dev: 0.05477225575051661; Max: 0.43
[INFO] [2019-07-12 14:40:00] Storing 6705 Nodes
[INFO] [2019-07-12 14:40:00] Processing group of 6705 in 7 groups of 1000
[INFO] [2019-07-12 14:40:03] Average Time: 0.294
[INFO] [2019-07-12 14:40:03] Total Time: 3s
[INFO] [2019-07-12 14:40:03] last 3 / first 3: 0.88
[INFO] [2019-07-12 14:40:03] Std.Dev: 0.044721359549995794; Max: 0.33
[INFO] [2019-07-12 14:40:03] Storing 5362 Occurrences
[INFO] [2019-07-12 14:40:03] Processing group of 5362 in 6 groups of 1000
[INFO] [2019-07-12 14:40:03] Average Time: 0.092
[INFO] [2019-07-12 14:40:03] Total Time: 1s
[INFO] [2019-07-12 14:40:03] Storing 2033 TraitsReferences
[INFO] [2019-07-12 14:40:03] Processing group of 2033 in 3 groups of 1000
[INFO] [2019-07-12 14:40:03] Average Time: 0.093
[INFO] [2019-07-12 14:40:03] Total Time: 1s
[INFO] [2019-07-12 14:40:03] Storing 5362 Traits
[INFO] [2019-07-12 14:40:03] Processing group of 5362 in 6 groups of 1000
[INFO] [2019-07-12 14:40:05] Average Time: 0.265
[INFO] [2019-07-12 14:40:05] Total Time: 2s
[INFO] [2019-07-12 14:40:05] Storing 14053 MetaTraits
[INFO] [2019-07-12 14:40:05] Processing group of 14053 in 15 groups of 1000
[INFO] [2019-07-12 14:40:07] Average Time: 0.113
[INFO] [2019-07-12 14:40:07] Total Time: 2s
[INFO] [2019-07-12 14:40:07] last 3 / first 3: 0.5
[INFO] [2019-07-12 14:40:07] Std.Dev: 0.03162277660168379; Max: 0.19
[STOP] [2019-07-12 14:40:07] parse_diff_and_store
[START] [2019-07-12 14:40:07] resolve_keys
[INFO] [2019-07-12 14:40:14] Occurrences to nodes (through scientific_names)...
[INFO] [2019-07-12 14:40:15] traits to occurrences...
[INFO] [2019-07-12 14:40:16] traits to nodes (through occurrences)...
[INFO] [2019-07-12 14:40:16] Traits to sex term...
[INFO] [2019-07-12 14:40:16] Traits to lifestage term...
[INFO] [2019-07-12 14:40:16] MetaTraits to traits...
[INFO] [2019-07-12 14:40:17] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-07-12 14:40:17] Assocs to occurrences...
[INFO] [2019-07-12 14:40:17] Assocs to nodes...
[INFO] [2019-07-12 14:40:17] Assoc to sex term...
[INFO] [2019-07-12 14:40:17] Assoc to lifestage term...
[STOP] [2019-07-12 14:40:17] resolve_keys
[START] [2019-07-12 14:40:17] hold_for_later_1
[STOP] [2019-07-12 14:40:17] hold_for_later_1
[START] [2019-07-12 14:40:17] hold_for_later_2
[STOP] [2019-07-12 14:40:17] hold_for_later_2
[START] [2019-07-12 14:40:17] resolve_missing_parents
[STOP] [2019-07-12 14:40:18] resolve_missing_parents
[START] [2019-07-12 14:40:18] rebuild_nodes
[START] [2019-07-12 14:40:18] Flattener#flatten
[START] [2019-07-12 14:40:18] Flattener#study_resource
[START] [2019-07-12 14:40:18] Flattener#build_ancestry
[STOP] [2019-07-12 14:40:19] Flattener#build_ancestry
[INFO] [2019-07-12 14:40:19] 6705 ancestry keys
[START] [2019-07-12 14:40:19] build_node_ancestors
[INFO] [2019-07-12 14:40:19] old ancestors deleted.
[STOP] [2019-07-12 14:40:22] build_node_ancestors
[START] [2019-07-12 14:40:24] Flattener#propagate_ancestor_ids
[STOP] [2019-07-12 14:40:25] Flattener#propagate_ancestor_ids
[STOP] [2019-07-12 14:40:25] Flattener#flatten
[STOP] [2019-07-12 14:40:25] rebuild_nodes
[START] [2019-07-12 14:40:25] resolve_missing_media_owners
[STOP] [2019-07-12 14:40:25] resolve_missing_media_owners
[START] [2019-07-12 14:40:25] sanitize_media_verbatims
[STOP] [2019-07-12 14:40:25] sanitize_media_verbatims
[START] [2019-07-12 14:40:25] queue_downloads
[STOP] [2019-07-12 14:40:25] queue_downloads
[START] [2019-07-12 14:40:25] parse_names
[WARN] [2019-07-12 14:40:25] I see 6705 names which still need to be parsed.
[STOP] [2019-07-12 14:40:31] parse_names
[START] [2019-07-12 14:40:31] denormalize_canonical_names_to_nodes
[STOP] [2019-07-12 14:40:31] denormalize_canonical_names_to_nodes
[START] [2019-07-12 14:40:31] match_nodes
[START] [2019-07-12 14:40:31] map_all_nodes_to_pages
[STOP] [2019-07-12 14:45:33] map_all_nodes_to_pages
[INFO] [2019-07-12 14:45:33] 125 Unmatched nodes (of 6705)! That's too many to output. First 10: Cricetulus tibetanus (#44160905); Handleyomys alfaroi (#44160984); Handleyomys melanotis (#44160988); Peromyscus schmidlyi (#44161417); Proedromys liangshanensis (#44161465); Wiedomys cerradensis (#44161638); Akodon philipmyersi (#44167482); Echimys vieirai (#44162143); Santamartamys rufodorsalis (#44162223); Coendou quichua (#44162342)
[START] [2019-07-12 14:45:33] update_nodes
[STOP] [2019-07-12 14:45:36] update_nodes
[STOP] [2019-07-12 14:45:36] match_nodes
[START] [2019-07-12 14:45:36] reindex_search
[STOP] [2019-07-12 14:45:48] reindex_search
[START] [2019-07-12 14:45:48] normalize_units
[STOP] [2019-07-12 14:45:48] normalize_units
[START] [2019-07-12 14:45:48] calculate_statistics
[STOP] [2019-07-12 14:45:48] calculate_statistics
[START] [2019-07-12 14:45:48] complete_harvest_instance
[START] [2019-07-12 14:45:48] overall_tsv_creation
[INFO] [2019-07-12 14:45:48] Processing group of 6705 in 1 batches of 10000
[INFO] [2019-07-12 14:47:09] 5362 Traits (unfiltered)...
[INFO] [2019-07-12 14:47:22] 5362 Traits (filtered)...
[INFO] [2019-07-12 14:47:22] 0 Associations (filtered)...
[INFO] [2019-07-12 14:48:07] 14053 metadata added.
[INFO] [2019-07-12 14:48:07] 0 metadata added.
[INFO] [2019-07-12 14:48:07] Average Time: 107.61
[INFO] [2019-07-12 14:48:07] Total Time: 2m19s
[STOP] [2019-07-12 14:48:07] overall_tsv_creation
[INFO] [2019-07-12 14:48:07] Done. Check your files:
[INFO] [2019-07-12 14:48:07] (6705 lines) /app/public/data/mam_diet/publish_nodes.tsv
[INFO] [2019-07-12 14:48:07] (38684 lines) /app/public/data/mam_diet/publish_node_ancestors.tsv
[INFO] [2019-07-12 14:48:07] (6705 lines) /app/public/data/mam_diet/publish_scientific_names.tsv
[INFO] [2019-07-12 14:48:07] (5363 lines) /app/public/data/mam_diet/publish_traits.tsv
[INFO] [2019-07-12 14:48:07] (14054 lines) /app/public/data/mam_diet/publish_metadata.tsv
[STOP] [2019-07-12 14:48:07] complete_harvest_instance
[START] [2019-07-12 14:48:07] completed
[STOP] [2019-07-12 14:48:07] completed
[STOP] [2019-07-12 14:48:07] logged process, took 522.95

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