Harvest for Andorra Species List Created 01 Oct 16:47

Stage: completed
Fetched: 01 Oct 16:47
Validated: 01 Oct 16:47
Deltas Created 01 Oct 16:48
Units Normalized: 01 Oct 16:55
Ancestry Built: 01 Oct 16:50
Nodes Matched: 01 Oct 16:55
Names Parsed: 01 Oct 16:50
New Models Stored: 01 Oct 16:49
Indexed: 01 Oct 16:55
Completed: 01 Oct 16:57
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-01 16:47:55 -0400 by logger.rb/56815
[START] [2019-10-01 16:47:55] logged process
[START] [2019-10-01 16:47:55] create_harvest_instance
[STOP] [2019-10-01 16:47:56] create_harvest_instance
[START] [2019-10-01 16:47:56] fetch_files
[STOP] [2019-10-01 16:47:56] fetch_files
[START] [2019-10-01 16:47:56] validate_each_file
[STOP] [2019-10-01 16:47:56] validate_each_file
[START] [2019-10-01 16:47:56] convert_to_csv
[CMD] [2019-10-01 16:47:56] /usr/bin/sort /app/public/converted_csv/andorra_sp_list_refs_14774.csv > /app/public/converted_csv/andorra_sp_list_refs_14774.csv_sorted
[CMD] [2019-10-01 16:47:58] /usr/bin/sort /app/public/converted_csv/andorra_sp_list_nodes_14775.csv > /app/public/converted_csv/andorra_sp_list_nodes_14775.csv_sorted
[CMD] [2019-10-01 16:47:59] /usr/bin/sort /app/public/converted_csv/andorra_sp_list_occurrences_14776.csv > /app/public/converted_csv/andorra_sp_list_occurrences_14776.csv_sorted
[CMD] [2019-10-01 16:48:01] /usr/bin/sort /app/public/converted_csv/andorra_sp_list_measurements_14777.csv > /app/public/converted_csv/andorra_sp_list_measurements_14777.csv_sorted
[STOP] [2019-10-01 16:48:02] convert_to_csv
[START] [2019-10-01 16:48:02] calculate_delta
[CMD] [2019-10-01 16:48:02] echo "0a" > /app/public/diff/andorra_sp_list_refs_14774.diff
[CMD] [2019-10-01 16:48:04] tail -n +1 /app/public/converted_csv/andorra_sp_list_refs_14774.csv >> /app/public/diff/andorra_sp_list_refs_14774.diff
[CMD] [2019-10-01 16:48:05] echo "." >> /app/public/diff/andorra_sp_list_refs_14774.diff
[CMD] [2019-10-01 16:48:07] echo "0a" > /app/public/diff/andorra_sp_list_nodes_14775.diff
[CMD] [2019-10-01 16:48:08] tail -n +1 /app/public/converted_csv/andorra_sp_list_nodes_14775.csv >> /app/public/diff/andorra_sp_list_nodes_14775.diff
[CMD] [2019-10-01 16:48:10] echo "." >> /app/public/diff/andorra_sp_list_nodes_14775.diff
[CMD] [2019-10-01 16:48:11] echo "0a" > /app/public/diff/andorra_sp_list_occurrences_14776.diff
[CMD] [2019-10-01 16:48:13] tail -n +1 /app/public/converted_csv/andorra_sp_list_occurrences_14776.csv >> /app/public/diff/andorra_sp_list_occurrences_14776.diff
[CMD] [2019-10-01 16:48:14] echo "." >> /app/public/diff/andorra_sp_list_occurrences_14776.diff
[CMD] [2019-10-01 16:48:16] echo "0a" > /app/public/diff/andorra_sp_list_measurements_14777.diff
[CMD] [2019-10-01 16:48:17] tail -n +1 /app/public/converted_csv/andorra_sp_list_measurements_14777.csv >> /app/public/diff/andorra_sp_list_measurements_14777.diff
[CMD] [2019-10-01 16:48:19] echo "." >> /app/public/diff/andorra_sp_list_measurements_14777.diff
[STOP] [2019-10-01 16:48:20] calculate_delta
[START] [2019-10-01 16:48:20] parse_diff_and_store
[INFO] [2019-10-01 16:48:22] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-01 16:48:23] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-01 16:48:27] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-01 16:48:29] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-01 16:48:54] Storing 2 References
[INFO] [2019-10-01 16:48:54] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-01 16:48:54] Average Time: 0.0
[INFO] [2019-10-01 16:48:54] Total Time: 1s
[INFO] [2019-10-01 16:48:54] Storing 6939 ScientificNames
[INFO] [2019-10-01 16:48:54] Processing group of 6939 in 7 groups of 1000
[INFO] [2019-10-01 16:48:56] Average Time: 0.346
[INFO] [2019-10-01 16:48:56] Total Time: 3s
[INFO] [2019-10-01 16:48:56] last 3 / first 3: 1.05
[INFO] [2019-10-01 16:48:56] Std.Dev: 0.03162277660168379; Max: 0.4
[INFO] [2019-10-01 16:48:56] Storing 6939 Nodes
[INFO] [2019-10-01 16:48:56] Processing group of 6939 in 7 groups of 1000
[INFO] [2019-10-01 16:48:58] Average Time: 0.281
[INFO] [2019-10-01 16:48:58] Total Time: 3s
[INFO] [2019-10-01 16:48:58] last 3 / first 3: 0.98
[INFO] [2019-10-01 16:48:58] Std.Dev: 0.0; Max: 0.32
[INFO] [2019-10-01 16:48:58] Storing 4338 Occurrences
[INFO] [2019-10-01 16:48:58] Processing group of 4338 in 5 groups of 1000
[INFO] [2019-10-01 16:48:59] Average Time: 0.1
[INFO] [2019-10-01 16:48:59] Total Time: 1s
[INFO] [2019-10-01 16:48:59] Storing 9036 TraitsReferences
[INFO] [2019-10-01 16:48:59] Processing group of 9036 in 10 groups of 1000
[INFO] [2019-10-01 16:48:59] Average Time: 0.067
[INFO] [2019-10-01 16:48:59] Total Time: 1s
[INFO] [2019-10-01 16:48:59] last 3 / first 3: 0.46
[INFO] [2019-10-01 16:48:59] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-01 16:48:59] Storing 9035 Traits
[INFO] [2019-10-01 16:48:59] Processing group of 9035 in 10 groups of 1000
[INFO] [2019-10-01 16:49:02] Average Time: 0.268
[INFO] [2019-10-01 16:49:02] Total Time: 3s
[INFO] [2019-10-01 16:49:02] last 3 / first 3: 0.59
[INFO] [2019-10-01 16:49:02] Std.Dev: 0.1; Max: 0.4
[INFO] [2019-10-01 16:49:02] Storing 9031 MetaTraits
[INFO] [2019-10-01 16:49:02] Processing group of 9031 in 10 groups of 1000
[INFO] [2019-10-01 16:49:03] Average Time: 0.109
[INFO] [2019-10-01 16:49:03] Total Time: 2s
[INFO] [2019-10-01 16:49:03] last 3 / first 3: 0.81
[INFO] [2019-10-01 16:49:03] Std.Dev: 0.044721359549995794; Max: 0.18
[STOP] [2019-10-01 16:49:03] parse_diff_and_store
[START] [2019-10-01 16:49:03] resolve_keys
[INFO] [2019-10-01 16:49:35] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-01 16:49:38] traits to occurrences...
[INFO] [2019-10-01 16:49:40] traits to nodes (through occurrences)...
[INFO] [2019-10-01 16:49:40] Traits to sex term...
[INFO] [2019-10-01 16:49:41] Traits to lifestage term...
[INFO] [2019-10-01 16:49:43] MetaTraits to traits...
[INFO] [2019-10-01 16:49:44] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-01 16:49:45] Assocs to occurrences...
[INFO] [2019-10-01 16:49:45] Assocs to nodes...
[INFO] [2019-10-01 16:49:45] Assoc to sex term...
[INFO] [2019-10-01 16:49:45] Assoc to lifestage term...
[STOP] [2019-10-01 16:49:45] resolve_keys
[START] [2019-10-01 16:49:45] hold_for_later_1
[STOP] [2019-10-01 16:49:45] hold_for_later_1
[START] [2019-10-01 16:49:45] hold_for_later_2
[STOP] [2019-10-01 16:49:45] hold_for_later_2
[START] [2019-10-01 16:49:45] resolve_missing_parents
[STOP] [2019-10-01 16:50:01] resolve_missing_parents
[START] [2019-10-01 16:50:01] rebuild_nodes
[START] [2019-10-01 16:50:01] Flattener#flatten
[START] [2019-10-01 16:50:01] Flattener#study_resource
[START] [2019-10-01 16:50:01] Flattener#build_ancestry
[STOP] [2019-10-01 16:50:03] Flattener#build_ancestry
[INFO] [2019-10-01 16:50:03] 6939 ancestry keys
[START] [2019-10-01 16:50:03] build_node_ancestors
[INFO] [2019-10-01 16:50:03] old ancestors deleted.
[STOP] [2019-10-01 16:50:03] build_node_ancestors
[START] [2019-10-01 16:50:04] Flattener#propagate_ancestor_ids
[STOP] [2019-10-01 16:50:04] Flattener#propagate_ancestor_ids
[STOP] [2019-10-01 16:50:04] Flattener#flatten
[STOP] [2019-10-01 16:50:04] rebuild_nodes
[START] [2019-10-01 16:50:04] resolve_missing_media_owners
[STOP] [2019-10-01 16:50:04] resolve_missing_media_owners
[START] [2019-10-01 16:50:05] sanitize_media_verbatims
[STOP] [2019-10-01 16:50:05] sanitize_media_verbatims
[START] [2019-10-01 16:50:05] queue_downloads
[STOP] [2019-10-01 16:50:05] queue_downloads
[START] [2019-10-01 16:50:05] parse_names
[WARN] [2019-10-01 16:50:05] I see 6939 names which still need to be parsed.
[STOP] [2019-10-01 16:50:10] parse_names
[START] [2019-10-01 16:50:10] denormalize_canonical_names_to_nodes
[STOP] [2019-10-01 16:50:10] denormalize_canonical_names_to_nodes
[START] [2019-10-01 16:50:10] match_nodes
[START] [2019-10-01 16:50:10] map_all_nodes_to_pages
[STOP] [2019-10-01 16:54:58] map_all_nodes_to_pages
[INFO] [2019-10-01 16:54:59] 447 Unmatched nodes (of 6939)! That's too many to output. First 10: Carex ovalis (#47362720); Carex viridula (#47366526); Carex hallerana (#47367909); Trichophorum cespitosus (#47362485); Trichophorum caespitosus (#47368222); Eleocharis caespitosus (#47369143); Scirpus cespitosus (#47363336); Kobresia (#47363639); Isolepis setaceus (#47368113); Poa variegata (#47364695)
[START] [2019-10-01 16:54:59] update_nodes
[STOP] [2019-10-01 16:55:01] update_nodes
[STOP] [2019-10-01 16:55:01] match_nodes
[START] [2019-10-01 16:55:01] reindex_search
[STOP] [2019-10-01 16:55:14] reindex_search
[START] [2019-10-01 16:55:14] normalize_units
[STOP] [2019-10-01 16:55:14] normalize_units
[START] [2019-10-01 16:55:14] calculate_statistics
[STOP] [2019-10-01 16:55:14] calculate_statistics
[START] [2019-10-01 16:55:14] complete_harvest_instance
[START] [2019-10-01 16:55:14] overall_tsv_creation
[INFO] [2019-10-01 16:55:14] Processing group of 6939 in 1 batches of 10000
[INFO] [2019-10-01 16:56:28] 4338 Traits (unfiltered)...
[INFO] [2019-10-01 16:56:41] 4338 Traits (filtered)...
[INFO] [2019-10-01 16:56:41] 0 Associations (filtered)...
[INFO] [2019-10-01 16:57:23] 21686 metadata added.
[INFO] [2019-10-01 16:57:23] 0 metadata added.
[INFO] [2019-10-01 16:57:23] Average Time: 102.01
[INFO] [2019-10-01 16:57:23] Total Time: 2m9s
[STOP] [2019-10-01 16:57:23] overall_tsv_creation
[INFO] [2019-10-01 16:57:23] Done. Check your files:
[INFO] [2019-10-01 16:57:25] (6939 lines) /app/public/data/andorra_sp_list/publish_nodes.tsv
[INFO] [2019-10-01 16:57:26] (10850 lines) /app/public/data/andorra_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-01 16:57:28] (6939 lines) /app/public/data/andorra_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-01 16:57:29] (4339 lines) /app/public/data/andorra_sp_list/publish_traits.tsv
[INFO] [2019-10-01 16:57:31] (21687 lines) /app/public/data/andorra_sp_list/publish_metadata.tsv
[STOP] [2019-10-01 16:57:31] complete_harvest_instance
[START] [2019-10-01 16:57:31] completed
[STOP] [2019-10-01 16:57:31] completed
[STOP] [2019-10-01 16:57:31] logged process, took 576.11
Latest Process

01 Oct 16:47 EXITED currently processing 0