Harvest for Sri Lanka Species List Created 16 Oct 07:09

Stage: completed
Fetched: 16 Oct 07:09
Validated: 16 Oct 07:09
Deltas Created 16 Oct 07:09
Units Normalized: 16 Oct 07:22
Ancestry Built: 16 Oct 07:11
Nodes Matched: 16 Oct 07:21
Names Parsed: 16 Oct 07:11
New Models Stored: 16 Oct 07:10
Indexed: 16 Oct 07:22
Completed: 16 Oct 07:26
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-16 07:09:00 -0400 by logger.rb/56815
[START] [2019-10-16 07:09:00] logged process
[START] [2019-10-16 07:09:00] create_harvest_instance
[STOP] [2019-10-16 07:09:00] create_harvest_instance
[START] [2019-10-16 07:09:00] fetch_files
[STOP] [2019-10-16 07:09:00] fetch_files
[START] [2019-10-16 07:09:00] validate_each_file
[STOP] [2019-10-16 07:09:02] validate_each_file
[START] [2019-10-16 07:09:02] convert_to_csv
[CMD] [2019-10-16 07:09:02] /usr/bin/sort /app/public/converted_csv/sri_lanka_sp_lis_refs_17333.csv > /app/public/converted_csv/sri_lanka_sp_lis_refs_17333.csv_sorted
[CMD] [2019-10-16 07:09:02] /usr/bin/sort /app/public/converted_csv/sri_lanka_sp_lis_nodes_17334.csv > /app/public/converted_csv/sri_lanka_sp_lis_nodes_17334.csv_sorted
[CMD] [2019-10-16 07:09:02] /usr/bin/sort /app/public/converted_csv/sri_lanka_sp_lis_occurrences_17335.csv > /app/public/converted_csv/sri_lanka_sp_lis_occurrences_17335.csv_sorted
[CMD] [2019-10-16 07:09:03] /usr/bin/sort /app/public/converted_csv/sri_lanka_sp_lis_measurements_17336.csv > /app/public/converted_csv/sri_lanka_sp_lis_measurements_17336.csv_sorted
[STOP] [2019-10-16 07:09:03] convert_to_csv
[START] [2019-10-16 07:09:03] calculate_delta
[CMD] [2019-10-16 07:09:03] echo "0a" > /app/public/diff/sri_lanka_sp_lis_refs_17333.diff
[CMD] [2019-10-16 07:09:03] tail -n +1 /app/public/converted_csv/sri_lanka_sp_lis_refs_17333.csv >> /app/public/diff/sri_lanka_sp_lis_refs_17333.diff
[CMD] [2019-10-16 07:09:04] echo "." >> /app/public/diff/sri_lanka_sp_lis_refs_17333.diff
[CMD] [2019-10-16 07:09:04] echo "0a" > /app/public/diff/sri_lanka_sp_lis_nodes_17334.diff
[CMD] [2019-10-16 07:09:04] tail -n +1 /app/public/converted_csv/sri_lanka_sp_lis_nodes_17334.csv >> /app/public/diff/sri_lanka_sp_lis_nodes_17334.diff
[CMD] [2019-10-16 07:09:04] echo "." >> /app/public/diff/sri_lanka_sp_lis_nodes_17334.diff
[CMD] [2019-10-16 07:09:05] echo "0a" > /app/public/diff/sri_lanka_sp_lis_occurrences_17335.diff
[CMD] [2019-10-16 07:09:05] tail -n +1 /app/public/converted_csv/sri_lanka_sp_lis_occurrences_17335.csv >> /app/public/diff/sri_lanka_sp_lis_occurrences_17335.diff
[CMD] [2019-10-16 07:09:05] echo "." >> /app/public/diff/sri_lanka_sp_lis_occurrences_17335.diff
[CMD] [2019-10-16 07:09:06] echo "0a" > /app/public/diff/sri_lanka_sp_lis_measurements_17336.diff
[CMD] [2019-10-16 07:09:06] tail -n +1 /app/public/converted_csv/sri_lanka_sp_lis_measurements_17336.csv >> /app/public/diff/sri_lanka_sp_lis_measurements_17336.diff
[CMD] [2019-10-16 07:09:06] echo "." >> /app/public/diff/sri_lanka_sp_lis_measurements_17336.diff
[STOP] [2019-10-16 07:09:06] calculate_delta
[START] [2019-10-16 07:09:06] parse_diff_and_store
[INFO] [2019-10-16 07:09:07] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 07:09:07] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 07:09:11] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 07:09:12] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 07:09:50] Storing 2 References
[INFO] [2019-10-16 07:09:50] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 07:09:50] Average Time: 0.0
[INFO] [2019-10-16 07:09:50] Total Time: 1s
[INFO] [2019-10-16 07:09:50] Storing 10939 ScientificNames
[INFO] [2019-10-16 07:09:50] Processing group of 10939 in 11 groups of 1000
[INFO] [2019-10-16 07:09:54] Average Time: 0.368
[INFO] [2019-10-16 07:09:54] Total Time: 5s
[INFO] [2019-10-16 07:09:54] last 3 / first 3: 0.85
[INFO] [2019-10-16 07:09:54] Std.Dev: 0.03162277660168379; Max: 0.44
[INFO] [2019-10-16 07:09:54] Storing 10939 Nodes
[INFO] [2019-10-16 07:09:54] Processing group of 10939 in 11 groups of 1000
[INFO] [2019-10-16 07:09:58] Average Time: 0.297
[INFO] [2019-10-16 07:09:58] Total Time: 4s
[INFO] [2019-10-16 07:09:58] last 3 / first 3: 0.97
[INFO] [2019-10-16 07:09:58] Std.Dev: 0.0; Max: 0.33
[INFO] [2019-10-16 07:09:58] Storing 6266 Occurrences
[INFO] [2019-10-16 07:09:58] Processing group of 6266 in 7 groups of 1000
[INFO] [2019-10-16 07:09:58] Average Time: 0.096
[INFO] [2019-10-16 07:09:58] Total Time: 1s
[INFO] [2019-10-16 07:09:58] last 3 / first 3: 0.68
[INFO] [2019-10-16 07:09:58] Std.Dev: 0.03162277660168379; Max: 0.13
[INFO] [2019-10-16 07:09:58] Storing 13110 TraitsReferences
[INFO] [2019-10-16 07:09:58] Processing group of 13110 in 14 groups of 1000
[INFO] [2019-10-16 07:09:59] Average Time: 0.071
[INFO] [2019-10-16 07:09:59] Total Time: 2s
[INFO] [2019-10-16 07:09:59] last 3 / first 3: 0.52
[INFO] [2019-10-16 07:09:59] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-16 07:09:59] Storing 13109 Traits
[INFO] [2019-10-16 07:09:59] Processing group of 13109 in 14 groups of 1000
[INFO] [2019-10-16 07:10:04] Average Time: 0.329
[INFO] [2019-10-16 07:10:04] Total Time: 5s
[INFO] [2019-10-16 07:10:04] last 3 / first 3: 0.51
[INFO] [2019-10-16 07:10:04] Std.Dev: 0.1224744871391589; Max: 0.52
[INFO] [2019-10-16 07:10:04] Storing 13094 MetaTraits
[INFO] [2019-10-16 07:10:04] Processing group of 13094 in 14 groups of 1000
[INFO] [2019-10-16 07:10:06] Average Time: 0.11
[INFO] [2019-10-16 07:10:06] Total Time: 2s
[INFO] [2019-10-16 07:10:06] last 3 / first 3: 0.58
[INFO] [2019-10-16 07:10:06] Std.Dev: 0.03162277660168379; Max: 0.15
[STOP] [2019-10-16 07:10:06] parse_diff_and_store
[START] [2019-10-16 07:10:06] resolve_keys
[INFO] [2019-10-16 07:10:46] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 07:10:50] traits to occurrences...
[INFO] [2019-10-16 07:10:55] traits to nodes (through occurrences)...
[INFO] [2019-10-16 07:10:55] Traits to sex term...
[INFO] [2019-10-16 07:10:58] Traits to lifestage term...
[INFO] [2019-10-16 07:11:03] MetaTraits to traits...
[INFO] [2019-10-16 07:11:03] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 07:11:05] Assocs to occurrences...
[INFO] [2019-10-16 07:11:05] Assocs to nodes...
[INFO] [2019-10-16 07:11:05] Assoc to sex term...
[INFO] [2019-10-16 07:11:05] Assoc to lifestage term...
[STOP] [2019-10-16 07:11:05] resolve_keys
[START] [2019-10-16 07:11:05] hold_for_later_1
[STOP] [2019-10-16 07:11:05] hold_for_later_1
[START] [2019-10-16 07:11:05] hold_for_later_2
[STOP] [2019-10-16 07:11:05] hold_for_later_2
[START] [2019-10-16 07:11:05] resolve_missing_parents
[STOP] [2019-10-16 07:11:26] resolve_missing_parents
[START] [2019-10-16 07:11:26] rebuild_nodes
[START] [2019-10-16 07:11:26] Flattener#flatten
[START] [2019-10-16 07:11:26] Flattener#study_resource
[START] [2019-10-16 07:11:26] Flattener#build_ancestry
[STOP] [2019-10-16 07:11:26] Flattener#build_ancestry
[INFO] [2019-10-16 07:11:26] 10939 ancestry keys
[START] [2019-10-16 07:11:26] build_node_ancestors
[INFO] [2019-10-16 07:11:26] old ancestors deleted.
[STOP] [2019-10-16 07:11:28] build_node_ancestors
[START] [2019-10-16 07:11:30] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 07:11:31] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 07:11:31] Flattener#flatten
[STOP] [2019-10-16 07:11:31] rebuild_nodes
[START] [2019-10-16 07:11:31] resolve_missing_media_owners
[STOP] [2019-10-16 07:11:31] resolve_missing_media_owners
[START] [2019-10-16 07:11:31] sanitize_media_verbatims
[STOP] [2019-10-16 07:11:31] sanitize_media_verbatims
[START] [2019-10-16 07:11:31] queue_downloads
[STOP] [2019-10-16 07:11:31] queue_downloads
[START] [2019-10-16 07:11:31] parse_names
[WARN] [2019-10-16 07:11:31] I see 10939 names which still need to be parsed.
[STOP] [2019-10-16 07:11:40] parse_names
[START] [2019-10-16 07:11:40] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 07:11:41] denormalize_canonical_names_to_nodes
[START] [2019-10-16 07:11:41] match_nodes
[START] [2019-10-16 07:11:41] map_all_nodes_to_pages
[STOP] [2019-10-16 07:21:50] map_all_nodes_to_pages
[INFO] [2019-10-16 07:21:50] 871 Unmatched nodes (of 10939)! That's too many to output. First 10: Sturnus pagodarum (#52204772); Muscicapa latirostris (#52195371); Saxicoloides fulicata (#52197998); Luscinia brunnea (#52198091); Cinnyris lotenia (#52195585); Cinnyris asiatica (#52196237); Nectarinia zeylonica (#52195561); Nectarinia lotenia (#52195594); Nectarinia asiatica (#52196203); Turdoides affinis (#52195057)
[START] [2019-10-16 07:21:50] update_nodes
[STOP] [2019-10-16 07:21:54] update_nodes
[STOP] [2019-10-16 07:21:54] match_nodes
[START] [2019-10-16 07:21:54] reindex_search
[STOP] [2019-10-16 07:22:24] reindex_search
[START] [2019-10-16 07:22:24] normalize_units
[STOP] [2019-10-16 07:22:24] normalize_units
[START] [2019-10-16 07:22:24] calculate_statistics
[STOP] [2019-10-16 07:22:24] calculate_statistics
[START] [2019-10-16 07:22:24] complete_harvest_instance
[START] [2019-10-16 07:22:24] overall_tsv_creation
[INFO] [2019-10-16 07:22:24] Processing group of 10939 in 2 batches of 10000
[INFO] [2019-10-16 07:23:52] 5870 Traits (unfiltered)...
[INFO] [2019-10-16 07:24:06] 5870 Traits (filtered)...
[INFO] [2019-10-16 07:24:06] 0 Associations (filtered)...
[INFO] [2019-10-16 07:24:54] 29337 metadata added.
[INFO] [2019-10-16 07:24:54] 0 metadata added.
[INFO] [2019-10-16 07:25:43] 396 Traits (unfiltered)...
[INFO] [2019-10-16 07:25:56] 396 Traits (filtered)...
[INFO] [2019-10-16 07:25:56] 0 Associations (filtered)...
[INFO] [2019-10-16 07:26:37] 1980 metadata added.
[INFO] [2019-10-16 07:26:37] 0 metadata added.
[INFO] [2019-10-16 07:26:37] Average Time: 102.595
[INFO] [2019-10-16 07:26:37] Total Time: 4m14s
[STOP] [2019-10-16 07:26:37] overall_tsv_creation
[INFO] [2019-10-16 07:26:37] Done. Check your files:
[INFO] [2019-10-16 07:26:37] (10939 lines) /app/public/data/sri_lanka_sp_lis/publish_nodes.tsv
[INFO] [2019-10-16 07:26:38] (25932 lines) /app/public/data/sri_lanka_sp_lis/publish_node_ancestors.tsv
[INFO] [2019-10-16 07:26:38] (10939 lines) /app/public/data/sri_lanka_sp_lis/publish_scientific_names.tsv
[INFO] [2019-10-16 07:26:38] (6267 lines) /app/public/data/sri_lanka_sp_lis/publish_traits.tsv
[INFO] [2019-10-16 07:26:39] (31318 lines) /app/public/data/sri_lanka_sp_lis/publish_metadata.tsv
[STOP] [2019-10-16 07:26:39] complete_harvest_instance
[START] [2019-10-16 07:26:39] completed
[STOP] [2019-10-16 07:26:39] completed
[STOP] [2019-10-16 07:26:39] logged process, took 1059.13
Latest Process

16 Oct 07:09 EXITED currently processing 0