Harvest for Honduras Species List Created 13 Oct 10:54

Stage: completed
Fetched: 13 Oct 10:54
Validated: 13 Oct 10:54
Deltas Created 13 Oct 10:54
Units Normalized: 13 Oct 10:56
Ancestry Built: 13 Oct 10:54
Nodes Matched: 13 Oct 10:56
Names Parsed: 13 Oct 10:54
New Models Stored: 13 Oct 10:54
Indexed: 13 Oct 10:56
Completed: 13 Oct 10:58
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-13 10:54:12 -0400 by logger.rb/56815
[START] [2019-10-13 10:54:12] logged process
[START] [2019-10-13 10:54:12] create_harvest_instance
[STOP] [2019-10-13 10:54:12] create_harvest_instance
[START] [2019-10-13 10:54:12] fetch_files
[STOP] [2019-10-13 10:54:12] fetch_files
[START] [2019-10-13 10:54:12] validate_each_file
[STOP] [2019-10-13 10:54:13] validate_each_file
[START] [2019-10-13 10:54:13] convert_to_csv
[CMD] [2019-10-13 10:54:13] /usr/bin/sort /app/public/converted_csv/honduras_sp_list_refs_16091.csv > /app/public/converted_csv/honduras_sp_list_refs_16091.csv_sorted
[CMD] [2019-10-13 10:54:13] /usr/bin/sort /app/public/converted_csv/honduras_sp_list_nodes_16092.csv > /app/public/converted_csv/honduras_sp_list_nodes_16092.csv_sorted
[CMD] [2019-10-13 10:54:13] /usr/bin/sort /app/public/converted_csv/honduras_sp_list_occurrences_16093.csv > /app/public/converted_csv/honduras_sp_list_occurrences_16093.csv_sorted
[CMD] [2019-10-13 10:54:13] /usr/bin/sort /app/public/converted_csv/honduras_sp_list_measurements_16094.csv > /app/public/converted_csv/honduras_sp_list_measurements_16094.csv_sorted
[STOP] [2019-10-13 10:54:13] convert_to_csv
[START] [2019-10-13 10:54:13] calculate_delta
[CMD] [2019-10-13 10:54:13] echo "0a" > /app/public/diff/honduras_sp_list_refs_16091.diff
[CMD] [2019-10-13 10:54:13] tail -n +1 /app/public/converted_csv/honduras_sp_list_refs_16091.csv >> /app/public/diff/honduras_sp_list_refs_16091.diff
[CMD] [2019-10-13 10:54:13] echo "." >> /app/public/diff/honduras_sp_list_refs_16091.diff
[CMD] [2019-10-13 10:54:13] echo "0a" > /app/public/diff/honduras_sp_list_nodes_16092.diff
[CMD] [2019-10-13 10:54:13] tail -n +1 /app/public/converted_csv/honduras_sp_list_nodes_16092.csv >> /app/public/diff/honduras_sp_list_nodes_16092.diff
[CMD] [2019-10-13 10:54:14] echo "." >> /app/public/diff/honduras_sp_list_nodes_16092.diff
[CMD] [2019-10-13 10:54:14] echo "0a" > /app/public/diff/honduras_sp_list_occurrences_16093.diff
[CMD] [2019-10-13 10:54:14] tail -n +1 /app/public/converted_csv/honduras_sp_list_occurrences_16093.csv >> /app/public/diff/honduras_sp_list_occurrences_16093.diff
[CMD] [2019-10-13 10:54:14] echo "." >> /app/public/diff/honduras_sp_list_occurrences_16093.diff
[CMD] [2019-10-13 10:54:14] echo "0a" > /app/public/diff/honduras_sp_list_measurements_16094.diff
[CMD] [2019-10-13 10:54:14] tail -n +1 /app/public/converted_csv/honduras_sp_list_measurements_16094.csv >> /app/public/diff/honduras_sp_list_measurements_16094.diff
[CMD] [2019-10-13 10:54:14] echo "." >> /app/public/diff/honduras_sp_list_measurements_16094.diff
[STOP] [2019-10-13 10:54:14] calculate_delta
[START] [2019-10-13 10:54:14] parse_diff_and_store
[INFO] [2019-10-13 10:54:14] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 10:54:14] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 10:54:15] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 10:54:15] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 10:54:19] Storing 2 References
[INFO] [2019-10-13 10:54:19] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 10:54:19] Average Time: 0.0
[INFO] [2019-10-13 10:54:19] Total Time: 1s
[INFO] [2019-10-13 10:54:19] Storing 1567 ScientificNames
[INFO] [2019-10-13 10:54:19] Processing group of 1567 in 2 groups of 1000
[INFO] [2019-10-13 10:54:20] Average Time: 0.33
[INFO] [2019-10-13 10:54:20] Total Time: 1s
[INFO] [2019-10-13 10:54:20] Storing 1567 Nodes
[INFO] [2019-10-13 10:54:20] Processing group of 1567 in 2 groups of 1000
[INFO] [2019-10-13 10:54:20] Average Time: 0.255
[INFO] [2019-10-13 10:54:20] Total Time: 1s
[INFO] [2019-10-13 10:54:20] Storing 482 Occurrences
[INFO] [2019-10-13 10:54:20] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-13 10:54:20] Average Time: 0.06
[INFO] [2019-10-13 10:54:20] Total Time: 1s
[INFO] [2019-10-13 10:54:20] Storing 1390 TraitsReferences
[INFO] [2019-10-13 10:54:20] Processing group of 1390 in 2 groups of 1000
[INFO] [2019-10-13 10:54:21] Average Time: 0.095
[INFO] [2019-10-13 10:54:21] Total Time: 1s
[INFO] [2019-10-13 10:54:21] Storing 1389 Traits
[INFO] [2019-10-13 10:54:21] Processing group of 1389 in 2 groups of 1000
[INFO] [2019-10-13 10:54:21] Average Time: 0.285
[INFO] [2019-10-13 10:54:21] Total Time: 1s
[INFO] [2019-10-13 10:54:21] Storing 1390 MetaTraits
[INFO] [2019-10-13 10:54:21] Processing group of 1390 in 2 groups of 1000
[INFO] [2019-10-13 10:54:21] Average Time: 0.1
[INFO] [2019-10-13 10:54:21] Total Time: 1s
[STOP] [2019-10-13 10:54:21] parse_diff_and_store
[START] [2019-10-13 10:54:21] resolve_keys
[INFO] [2019-10-13 10:54:30] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 10:54:30] traits to occurrences...
[INFO] [2019-10-13 10:54:31] traits to nodes (through occurrences)...
[INFO] [2019-10-13 10:54:31] Traits to sex term...
[INFO] [2019-10-13 10:54:31] Traits to lifestage term...
[INFO] [2019-10-13 10:54:31] MetaTraits to traits...
[INFO] [2019-10-13 10:54:31] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 10:54:31] Assocs to occurrences...
[INFO] [2019-10-13 10:54:31] Assocs to nodes...
[INFO] [2019-10-13 10:54:31] Assoc to sex term...
[INFO] [2019-10-13 10:54:31] Assoc to lifestage term...
[STOP] [2019-10-13 10:54:31] resolve_keys
[START] [2019-10-13 10:54:31] hold_for_later_1
[STOP] [2019-10-13 10:54:31] hold_for_later_1
[START] [2019-10-13 10:54:31] hold_for_later_2
[STOP] [2019-10-13 10:54:31] hold_for_later_2
[START] [2019-10-13 10:54:31] resolve_missing_parents
[STOP] [2019-10-13 10:54:33] resolve_missing_parents
[START] [2019-10-13 10:54:33] rebuild_nodes
[START] [2019-10-13 10:54:33] Flattener#flatten
[START] [2019-10-13 10:54:33] Flattener#study_resource
[START] [2019-10-13 10:54:33] Flattener#build_ancestry
[STOP] [2019-10-13 10:54:33] Flattener#build_ancestry
[INFO] [2019-10-13 10:54:33] 1567 ancestry keys
[START] [2019-10-13 10:54:33] build_node_ancestors
[INFO] [2019-10-13 10:54:33] old ancestors deleted.
[STOP] [2019-10-13 10:54:33] build_node_ancestors
[START] [2019-10-13 10:54:34] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 10:54:34] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 10:54:34] Flattener#flatten
[STOP] [2019-10-13 10:54:34] rebuild_nodes
[START] [2019-10-13 10:54:34] resolve_missing_media_owners
[STOP] [2019-10-13 10:54:34] resolve_missing_media_owners
[START] [2019-10-13 10:54:34] sanitize_media_verbatims
[STOP] [2019-10-13 10:54:34] sanitize_media_verbatims
[START] [2019-10-13 10:54:34] queue_downloads
[STOP] [2019-10-13 10:54:34] queue_downloads
[START] [2019-10-13 10:54:34] parse_names
[WARN] [2019-10-13 10:54:34] I see 1567 names which still need to be parsed.
[STOP] [2019-10-13 10:54:36] parse_names
[START] [2019-10-13 10:54:36] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 10:54:36] denormalize_canonical_names_to_nodes
[START] [2019-10-13 10:54:36] match_nodes
[START] [2019-10-13 10:54:36] map_all_nodes_to_pages
[STOP] [2019-10-13 10:56:16] map_all_nodes_to_pages
[INFO] [2019-10-13 10:56:16] 46 Unmatched nodes (of 1567)! That's too many to output. First 10: Seiurus aurocapillus (#50071213); Oreothlypis peregrina (#50070259); Dendroica (#50070614); Dendroica coronata (#50070613); Dendroica petechia (#50071064); Wilsonia citrina (#50070816); Coerebidae (#50070186); Thalaseus (#50070043); Thalaseus maximus (#50070042); Porphyrio martinicus (#50071214)
[START] [2019-10-13 10:56:16] update_nodes
[STOP] [2019-10-13 10:56:16] update_nodes
[STOP] [2019-10-13 10:56:16] match_nodes
[START] [2019-10-13 10:56:16] reindex_search
[STOP] [2019-10-13 10:56:20] reindex_search
[START] [2019-10-13 10:56:20] normalize_units
[STOP] [2019-10-13 10:56:20] normalize_units
[START] [2019-10-13 10:56:20] calculate_statistics
[STOP] [2019-10-13 10:56:20] calculate_statistics
[START] [2019-10-13 10:56:20] complete_harvest_instance
[START] [2019-10-13 10:56:20] overall_tsv_creation
[INFO] [2019-10-13 10:56:20] Processing group of 1567 in 1 batches of 10000
[INFO] [2019-10-13 10:57:12] 482 Traits (unfiltered)...
[INFO] [2019-10-13 10:57:26] 482 Traits (filtered)...
[INFO] [2019-10-13 10:57:26] 0 Associations (filtered)...
[INFO] [2019-10-13 10:58:03] 2410 metadata added.
[INFO] [2019-10-13 10:58:03] 0 metadata added.
[INFO] [2019-10-13 10:58:03] Average Time: 81.22
[INFO] [2019-10-13 10:58:03] Total Time: 1m43s
[STOP] [2019-10-13 10:58:03] overall_tsv_creation
[INFO] [2019-10-13 10:58:03] Done. Check your files:
[INFO] [2019-10-13 10:58:03] (1567 lines) /app/public/data/honduras_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 10:58:03] (4625 lines) /app/public/data/honduras_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 10:58:03] (1567 lines) /app/public/data/honduras_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 10:58:03] (483 lines) /app/public/data/honduras_sp_list/publish_traits.tsv
[INFO] [2019-10-13 10:58:04] (2411 lines) /app/public/data/honduras_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 10:58:04] complete_harvest_instance
[START] [2019-10-13 10:58:04] completed
[STOP] [2019-10-13 10:58:04] completed
[STOP] [2019-10-13 10:58:04] logged process, took 231.59
Latest Process

13 Oct 10:54 EXITED currently processing 0