Harvest for Romania Species List Created 15 Oct 14:28

Stage: completed
Fetched: 15 Oct 14:28
Validated: 15 Oct 14:28
Deltas Created 15 Oct 14:28
Units Normalized: 15 Oct 14:42
Ancestry Built: 15 Oct 14:30
Nodes Matched: 15 Oct 14:41
Names Parsed: 15 Oct 14:30
New Models Stored: 15 Oct 14:29
Indexed: 15 Oct 14:42
Completed: 15 Oct 14:45
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-15 14:28:01 -0400 by logger.rb/56815
[START] [2019-10-15 14:28:01] logged process
[START] [2019-10-15 14:28:01] create_harvest_instance
[STOP] [2019-10-15 14:28:01] create_harvest_instance
[START] [2019-10-15 14:28:01] fetch_files
[STOP] [2019-10-15 14:28:01] fetch_files
[START] [2019-10-15 14:28:01] validate_each_file
[STOP] [2019-10-15 14:28:02] validate_each_file
[START] [2019-10-15 14:28:02] convert_to_csv
[CMD] [2019-10-15 14:28:02] /usr/bin/sort /app/public/converted_csv/romania_sp_list_refs_16997.csv > /app/public/converted_csv/romania_sp_list_refs_16997.csv_sorted
[CMD] [2019-10-15 14:28:03] /usr/bin/sort /app/public/converted_csv/romania_sp_list_nodes_16998.csv > /app/public/converted_csv/romania_sp_list_nodes_16998.csv_sorted
[CMD] [2019-10-15 14:28:03] /usr/bin/sort /app/public/converted_csv/romania_sp_list_occurrences_16999.csv > /app/public/converted_csv/romania_sp_list_occurrences_16999.csv_sorted
[CMD] [2019-10-15 14:28:03] /usr/bin/sort /app/public/converted_csv/romania_sp_list_measurements_17000.csv > /app/public/converted_csv/romania_sp_list_measurements_17000.csv_sorted
[STOP] [2019-10-15 14:28:04] convert_to_csv
[START] [2019-10-15 14:28:04] calculate_delta
[CMD] [2019-10-15 14:28:04] echo "0a" > /app/public/diff/romania_sp_list_refs_16997.diff
[CMD] [2019-10-15 14:28:04] tail -n +1 /app/public/converted_csv/romania_sp_list_refs_16997.csv >> /app/public/diff/romania_sp_list_refs_16997.diff
[CMD] [2019-10-15 14:28:04] echo "." >> /app/public/diff/romania_sp_list_refs_16997.diff
[CMD] [2019-10-15 14:28:04] echo "0a" > /app/public/diff/romania_sp_list_nodes_16998.diff
[CMD] [2019-10-15 14:28:05] tail -n +1 /app/public/converted_csv/romania_sp_list_nodes_16998.csv >> /app/public/diff/romania_sp_list_nodes_16998.diff
[CMD] [2019-10-15 14:28:05] echo "." >> /app/public/diff/romania_sp_list_nodes_16998.diff
[CMD] [2019-10-15 14:28:05] echo "0a" > /app/public/diff/romania_sp_list_occurrences_16999.diff
[CMD] [2019-10-15 14:28:06] tail -n +1 /app/public/converted_csv/romania_sp_list_occurrences_16999.csv >> /app/public/diff/romania_sp_list_occurrences_16999.diff
[CMD] [2019-10-15 14:28:06] echo "." >> /app/public/diff/romania_sp_list_occurrences_16999.diff
[CMD] [2019-10-15 14:28:06] echo "0a" > /app/public/diff/romania_sp_list_measurements_17000.diff
[CMD] [2019-10-15 14:28:06] tail -n +1 /app/public/converted_csv/romania_sp_list_measurements_17000.csv >> /app/public/diff/romania_sp_list_measurements_17000.diff
[CMD] [2019-10-15 14:28:07] echo "." >> /app/public/diff/romania_sp_list_measurements_17000.diff
[STOP] [2019-10-15 14:28:07] calculate_delta
[START] [2019-10-15 14:28:07] parse_diff_and_store
[INFO] [2019-10-15 14:28:07] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 14:28:08] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 14:28:12] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 14:28:13] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 14:28:48] Storing 2 References
[INFO] [2019-10-15 14:28:48] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 14:28:48] Average Time: 0.0
[INFO] [2019-10-15 14:28:48] Total Time: 1s
[INFO] [2019-10-15 14:28:48] Storing 10250 ScientificNames
[INFO] [2019-10-15 14:28:48] Processing group of 10250 in 11 groups of 1000
[INFO] [2019-10-15 14:28:52] Average Time: 0.359
[INFO] [2019-10-15 14:28:52] Total Time: 4s
[INFO] [2019-10-15 14:28:52] last 3 / first 3: 0.78
[INFO] [2019-10-15 14:28:52] Std.Dev: 0.1; Max: 0.47
[INFO] [2019-10-15 14:28:52] Storing 10250 Nodes
[INFO] [2019-10-15 14:28:52] Processing group of 10250 in 11 groups of 1000
[INFO] [2019-10-15 14:28:56] Average Time: 0.281
[INFO] [2019-10-15 14:28:56] Total Time: 4s
[INFO] [2019-10-15 14:28:56] last 3 / first 3: 0.82
[INFO] [2019-10-15 14:28:56] Std.Dev: 0.07071067811865475; Max: 0.36
[INFO] [2019-10-15 14:28:56] Storing 5784 Occurrences
[INFO] [2019-10-15 14:28:56] Processing group of 5784 in 6 groups of 1000
[INFO] [2019-10-15 14:28:56] Average Time: 0.103
[INFO] [2019-10-15 14:28:56] Total Time: 1s
[INFO] [2019-10-15 14:28:56] Storing 12120 TraitsReferences
[INFO] [2019-10-15 14:28:56] Processing group of 12120 in 13 groups of 1000
[INFO] [2019-10-15 14:28:57] Average Time: 0.069
[INFO] [2019-10-15 14:28:57] Total Time: 1s
[INFO] [2019-10-15 14:28:57] last 3 / first 3: 0.52
[INFO] [2019-10-15 14:28:57] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-15 14:28:57] Storing 12119 Traits
[INFO] [2019-10-15 14:28:57] Processing group of 12119 in 13 groups of 1000
[INFO] [2019-10-15 14:29:01] Average Time: 0.288
[INFO] [2019-10-15 14:29:01] Total Time: 4s
[INFO] [2019-10-15 14:29:01] last 3 / first 3: 0.59
[INFO] [2019-10-15 14:29:01] Std.Dev: 0.08944271909999159; Max: 0.45
[INFO] [2019-10-15 14:29:01] Storing 12106 MetaTraits
[INFO] [2019-10-15 14:29:01] Processing group of 12106 in 13 groups of 1000
[INFO] [2019-10-15 14:29:03] Average Time: 0.112
[INFO] [2019-10-15 14:29:03] Total Time: 2s
[INFO] [2019-10-15 14:29:03] last 3 / first 3: 0.64
[INFO] [2019-10-15 14:29:03] Std.Dev: 0.03162277660168379; Max: 0.18
[STOP] [2019-10-15 14:29:03] parse_diff_and_store
[START] [2019-10-15 14:29:03] resolve_keys
[INFO] [2019-10-15 14:29:41] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 14:29:44] traits to occurrences...
[INFO] [2019-10-15 14:29:49] traits to nodes (through occurrences)...
[INFO] [2019-10-15 14:29:49] Traits to sex term...
[INFO] [2019-10-15 14:29:53] Traits to lifestage term...
[INFO] [2019-10-15 14:29:57] MetaTraits to traits...
[INFO] [2019-10-15 14:29:57] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 14:29:59] Assocs to occurrences...
[INFO] [2019-10-15 14:29:59] Assocs to nodes...
[INFO] [2019-10-15 14:29:59] Assoc to sex term...
[INFO] [2019-10-15 14:29:59] Assoc to lifestage term...
[STOP] [2019-10-15 14:29:59] resolve_keys
[START] [2019-10-15 14:29:59] hold_for_later_1
[STOP] [2019-10-15 14:29:59] hold_for_later_1
[START] [2019-10-15 14:29:59] hold_for_later_2
[STOP] [2019-10-15 14:29:59] hold_for_later_2
[START] [2019-10-15 14:29:59] resolve_missing_parents
[STOP] [2019-10-15 14:30:18] resolve_missing_parents
[START] [2019-10-15 14:30:18] rebuild_nodes
[START] [2019-10-15 14:30:18] Flattener#flatten
[START] [2019-10-15 14:30:18] Flattener#study_resource
[START] [2019-10-15 14:30:18] Flattener#build_ancestry
[STOP] [2019-10-15 14:30:19] Flattener#build_ancestry
[INFO] [2019-10-15 14:30:19] 10250 ancestry keys
[START] [2019-10-15 14:30:19] build_node_ancestors
[INFO] [2019-10-15 14:30:19] old ancestors deleted.
[STOP] [2019-10-15 14:30:21] build_node_ancestors
[START] [2019-10-15 14:30:24] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 14:30:25] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 14:30:25] Flattener#flatten
[STOP] [2019-10-15 14:30:25] rebuild_nodes
[START] [2019-10-15 14:30:25] resolve_missing_media_owners
[STOP] [2019-10-15 14:30:25] resolve_missing_media_owners
[START] [2019-10-15 14:30:25] sanitize_media_verbatims
[STOP] [2019-10-15 14:30:25] sanitize_media_verbatims
[START] [2019-10-15 14:30:25] queue_downloads
[STOP] [2019-10-15 14:30:25] queue_downloads
[START] [2019-10-15 14:30:25] parse_names
[WARN] [2019-10-15 14:30:25] I see 10250 names which still need to be parsed.
[STOP] [2019-10-15 14:30:34] parse_names
[START] [2019-10-15 14:30:34] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 14:30:34] denormalize_canonical_names_to_nodes
[START] [2019-10-15 14:30:34] match_nodes
[START] [2019-10-15 14:30:34] map_all_nodes_to_pages
[STOP] [2019-10-15 14:41:40] map_all_nodes_to_pages
[INFO] [2019-10-15 14:41:40] 1185 Unmatched nodes (of 10250)! That's too many to output. First 10: Hordeum distichum (#51710214); Festuca pratensis (#51702207); Phleum ambiguum (#51710333); Agrostis tenuis (#51701968); Thinopyrum hispidus (#51702711); Bromus mollis (#51707162); Crypsis schoenoides (#51709858); Elymus trichophorum (#51709423); Elymus intermedium (#51709586); Aegilops triaristata (#51707040)
[START] [2019-10-15 14:41:40] update_nodes
[STOP] [2019-10-15 14:41:44] update_nodes
[STOP] [2019-10-15 14:41:44] match_nodes
[START] [2019-10-15 14:41:44] reindex_search
[STOP] [2019-10-15 14:42:12] reindex_search
[START] [2019-10-15 14:42:12] normalize_units
[STOP] [2019-10-15 14:42:12] normalize_units
[START] [2019-10-15 14:42:12] calculate_statistics
[STOP] [2019-10-15 14:42:13] calculate_statistics
[START] [2019-10-15 14:42:13] complete_harvest_instance
[START] [2019-10-15 14:42:13] overall_tsv_creation
[INFO] [2019-10-15 14:42:13] Processing group of 10250 in 2 batches of 10000
[INFO] [2019-10-15 14:43:42] 5784 Traits (unfiltered)...
[INFO] [2019-10-15 14:43:56] 5784 Traits (filtered)...
[INFO] [2019-10-15 14:43:56] 0 Associations (filtered)...
[INFO] [2019-10-15 14:44:45] 28908 metadata added.
[INFO] [2019-10-15 14:44:45] 0 metadata added.
[INFO] [2019-10-15 14:45:18] Average Time: 68.51
[INFO] [2019-10-15 14:45:18] Total Time: 3m6s
[STOP] [2019-10-15 14:45:18] overall_tsv_creation
[INFO] [2019-10-15 14:45:18] Done. Check your files:
[INFO] [2019-10-15 14:45:18] (10250 lines) /app/public/data/romania_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 14:45:19] (34374 lines) /app/public/data/romania_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 14:45:19] (10250 lines) /app/public/data/romania_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 14:45:19] (5785 lines) /app/public/data/romania_sp_list/publish_traits.tsv
[INFO] [2019-10-15 14:45:19] (28909 lines) /app/public/data/romania_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 14:45:20] complete_harvest_instance
[START] [2019-10-15 14:45:20] completed
[STOP] [2019-10-15 14:45:20] completed
[STOP] [2019-10-15 14:45:20] logged process, took 1039.19
Latest Process

15 Oct 14:28 EXITED currently processing 0