Harvest for Listed Species in Texas Created 16 Jul 12:56

Stage: completed
Fetched: 16 Jul 12:56
Validated: 16 Jul 12:56
Deltas Created 16 Jul 12:56
Units Normalized: 16 Jul 12:57
Ancestry Built: 16 Jul 12:56
Nodes Matched: 16 Jul 12:57
Names Parsed: 16 Jul 12:56
New Models Stored: 16 Jul 12:56
Indexed: 16 Jul 12:57
Completed: 16 Jul 12:59
Time to Harvest: less than a minute
Harvesting Log

(126 lines)
# Logfile created on 2019-07-16 12:56:21 -0400 by logger.rb/56815
[START] [2019-07-16 12:56:21] logged process
[START] [2019-07-16 12:56:21] create_harvest_instance
[STOP] [2019-07-16 12:56:22] create_harvest_instance
[START] [2019-07-16 12:56:22] fetch_files
[STOP] [2019-07-16 12:56:22] fetch_files
[START] [2019-07-16 12:56:22] validate_each_file
[STOP] [2019-07-16 12:56:22] validate_each_file
[START] [2019-07-16 12:56:22] convert_to_csv
[CMD] [2019-07-16 12:56:22] /usr/bin/sort /app/public/converted_csv/listed_sp_texas_nodes_14251.csv > /app/public/converted_csv/listed_sp_texas_nodes_14251.csv_sorted
[CMD] [2019-07-16 12:56:23] /usr/bin/sort /app/public/converted_csv/listed_sp_texas_occurrences_14252.csv > /app/public/converted_csv/listed_sp_texas_occurrences_14252.csv_sorted
[CMD] [2019-07-16 12:56:25] /usr/bin/sort /app/public/converted_csv/listed_sp_texas_measurements_14253.csv > /app/public/converted_csv/listed_sp_texas_measurements_14253.csv_sorted
[STOP] [2019-07-16 12:56:27] convert_to_csv
[START] [2019-07-16 12:56:27] calculate_delta
[CMD] [2019-07-16 12:56:27] echo "0a" > /app/public/diff/listed_sp_texas_nodes_14251.diff
[CMD] [2019-07-16 12:56:28] tail -n +1 /app/public/converted_csv/listed_sp_texas_nodes_14251.csv >> /app/public/diff/listed_sp_texas_nodes_14251.diff
[CMD] [2019-07-16 12:56:30] echo "." >> /app/public/diff/listed_sp_texas_nodes_14251.diff
[CMD] [2019-07-16 12:56:31] echo "0a" > /app/public/diff/listed_sp_texas_occurrences_14252.diff
[CMD] [2019-07-16 12:56:33] tail -n +1 /app/public/converted_csv/listed_sp_texas_occurrences_14252.csv >> /app/public/diff/listed_sp_texas_occurrences_14252.diff
[CMD] [2019-07-16 12:56:35] echo "." >> /app/public/diff/listed_sp_texas_occurrences_14252.diff
[CMD] [2019-07-16 12:56:36] echo "0a" > /app/public/diff/listed_sp_texas_measurements_14253.diff
[CMD] [2019-07-16 12:56:38] tail -n +1 /app/public/converted_csv/listed_sp_texas_measurements_14253.csv >> /app/public/diff/listed_sp_texas_measurements_14253.diff
[CMD] [2019-07-16 12:56:40] echo "." >> /app/public/diff/listed_sp_texas_measurements_14253.diff
[STOP] [2019-07-16 12:56:41] calculate_delta
[START] [2019-07-16 12:56:41] parse_diff_and_store
[INFO] [2019-07-16 12:56:43] Loading nodes diff file into memory (true lines)...
[INFO] [2019-07-16 12:56:45] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-07-16 12:56:46] Loading measurements diff file into memory (true lines)...
[INFO] [2019-07-16 12:56:47] Storing 416 ScientificNames
[INFO] [2019-07-16 12:56:47] Processing group of 416 in 1 groups of 1000
[INFO] [2019-07-16 12:56:47] Average Time: 0.21
[INFO] [2019-07-16 12:56:47] Total Time: 1s
[INFO] [2019-07-16 12:56:47] Storing 416 Nodes
[INFO] [2019-07-16 12:56:47] Processing group of 416 in 1 groups of 1000
[INFO] [2019-07-16 12:56:48] Average Time: 0.18
[INFO] [2019-07-16 12:56:48] Total Time: 1s
[INFO] [2019-07-16 12:56:48] Storing 213 Occurrences
[INFO] [2019-07-16 12:56:48] Processing group of 213 in 1 groups of 1000
[INFO] [2019-07-16 12:56:48] Average Time: 0.03
[INFO] [2019-07-16 12:56:48] Total Time: 1s
[INFO] [2019-07-16 12:56:48] Storing 213 Traits
[INFO] [2019-07-16 12:56:48] Processing group of 213 in 1 groups of 1000
[INFO] [2019-07-16 12:56:48] Average Time: 0.15
[INFO] [2019-07-16 12:56:48] Total Time: 1s
[INFO] [2019-07-16 12:56:48] Storing 426 MetaTraits
[INFO] [2019-07-16 12:56:48] Processing group of 426 in 1 groups of 1000
[INFO] [2019-07-16 12:56:48] Average Time: 0.07
[INFO] [2019-07-16 12:56:48] Total Time: 1s
[STOP] [2019-07-16 12:56:48] parse_diff_and_store
[START] [2019-07-16 12:56:48] resolve_keys
[INFO] [2019-07-16 12:56:52] Occurrences to nodes (through scientific_names)...
[INFO] [2019-07-16 12:56:52] traits to occurrences...
[INFO] [2019-07-16 12:56:52] traits to nodes (through occurrences)...
[INFO] [2019-07-16 12:56:52] Traits to sex term...
[INFO] [2019-07-16 12:56:52] Traits to lifestage term...
[INFO] [2019-07-16 12:56:52] MetaTraits to traits...
[INFO] [2019-07-16 12:56:52] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-07-16 12:56:52] Assocs to occurrences...
[INFO] [2019-07-16 12:56:52] Assocs to nodes...
[INFO] [2019-07-16 12:56:52] Assoc to sex term...
[INFO] [2019-07-16 12:56:52] Assoc to lifestage term...
[STOP] [2019-07-16 12:56:52] resolve_keys
[START] [2019-07-16 12:56:52] hold_for_later_1
[STOP] [2019-07-16 12:56:52] hold_for_later_1
[START] [2019-07-16 12:56:52] hold_for_later_2
[STOP] [2019-07-16 12:56:52] hold_for_later_2
[START] [2019-07-16 12:56:52] resolve_missing_parents
[STOP] [2019-07-16 12:56:52] resolve_missing_parents
[START] [2019-07-16 12:56:52] rebuild_nodes
[START] [2019-07-16 12:56:52] Flattener#flatten
[START] [2019-07-16 12:56:52] Flattener#study_resource
[START] [2019-07-16 12:56:52] Flattener#build_ancestry
[STOP] [2019-07-16 12:56:52] Flattener#build_ancestry
[INFO] [2019-07-16 12:56:52] 416 ancestry keys
[START] [2019-07-16 12:56:52] build_node_ancestors
[INFO] [2019-07-16 12:56:52] old ancestors deleted.
[STOP] [2019-07-16 12:56:52] build_node_ancestors
[START] [2019-07-16 12:56:52] Flattener#propagate_ancestor_ids
[STOP] [2019-07-16 12:56:52] Flattener#propagate_ancestor_ids
[STOP] [2019-07-16 12:56:52] Flattener#flatten
[STOP] [2019-07-16 12:56:52] rebuild_nodes
[START] [2019-07-16 12:56:52] resolve_missing_media_owners
[STOP] [2019-07-16 12:56:52] resolve_missing_media_owners
[START] [2019-07-16 12:56:52] sanitize_media_verbatims
[STOP] [2019-07-16 12:56:52] sanitize_media_verbatims
[START] [2019-07-16 12:56:52] queue_downloads
[STOP] [2019-07-16 12:56:52] queue_downloads
[START] [2019-07-16 12:56:52] parse_names
[WARN] [2019-07-16 12:56:52] I see 416 names which still need to be parsed.
[STOP] [2019-07-16 12:56:54] parse_names
[START] [2019-07-16 12:56:54] denormalize_canonical_names_to_nodes
[STOP] [2019-07-16 12:56:54] denormalize_canonical_names_to_nodes
[START] [2019-07-16 12:56:54] match_nodes
[START] [2019-07-16 12:56:54] map_all_nodes_to_pages
[STOP] [2019-07-16 12:57:24] map_all_nodes_to_pages
[INFO] [2019-07-16 12:57:24] 17 Unmatched nodes (of 416)! That's too many to output. First 10: Siren (#44581656); Aimophila aestivalis (#44581790); Dendroica (#44581847); Dendroica chrysoparia (#44581848); Sterna antillarum athalassos (#44581852); Picoides borealis (#44581864); Parula (#44581880); Parula pitiayumi (#44581881); Coccyzus americanus occidentails (#44581883); Gammarus hyalleloides (#44581971)
[START] [2019-07-16 12:57:24] update_nodes
[STOP] [2019-07-16 12:57:24] update_nodes
[STOP] [2019-07-16 12:57:24] match_nodes
[START] [2019-07-16 12:57:24] reindex_search
[STOP] [2019-07-16 12:57:25] reindex_search
[START] [2019-07-16 12:57:25] normalize_units
[STOP] [2019-07-16 12:57:25] normalize_units
[START] [2019-07-16 12:57:25] calculate_statistics
[STOP] [2019-07-16 12:57:25] calculate_statistics
[START] [2019-07-16 12:57:25] complete_harvest_instance
[START] [2019-07-16 12:57:25] overall_tsv_creation
[INFO] [2019-07-16 12:57:25] Processing group of 416 in 1 batches of 10000
[INFO] [2019-07-16 12:58:10] 213 Traits (unfiltered)...
[INFO] [2019-07-16 12:58:23] 213 Traits (filtered)...
[INFO] [2019-07-16 12:58:23] 0 Associations (filtered)...
[INFO] [2019-07-16 12:58:58] 426 metadata added.
[INFO] [2019-07-16 12:58:58] 0 metadata added.
[INFO] [2019-07-16 12:58:58] Average Time: 71.89
[INFO] [2019-07-16 12:58:58] Total Time: 1m33s
[STOP] [2019-07-16 12:58:58] overall_tsv_creation
[INFO] [2019-07-16 12:58:58] Done. Check your files:
[INFO] [2019-07-16 12:59:00] (416 lines) /app/public/data/listed_sp_texas/publish_nodes.tsv
[INFO] [2019-07-16 12:59:01] (1537 lines) /app/public/data/listed_sp_texas/publish_node_ancestors.tsv
[INFO] [2019-07-16 12:59:03] (416 lines) /app/public/data/listed_sp_texas/publish_scientific_names.tsv
[INFO] [2019-07-16 12:59:05] (214 lines) /app/public/data/listed_sp_texas/publish_traits.tsv
[INFO] [2019-07-16 12:59:06] (427 lines) /app/public/data/listed_sp_texas/publish_metadata.tsv
[STOP] [2019-07-16 12:59:06] complete_harvest_instance
[START] [2019-07-16 12:59:06] completed
[STOP] [2019-07-16 12:59:06] completed
[STOP] [2019-07-16 12:59:06] logged process, took 165.22
Latest Process

16 Jul 12:56 EXITED currently processing 0