Harvest for Zambia Species List Created 17 Oct 11:33

Stage: completed
Fetched: 17 Oct 11:33
Validated: 17 Oct 11:33
Deltas Created 17 Oct 11:33
Units Normalized: 17 Oct 11:41
Ancestry Built: 17 Oct 11:35
Nodes Matched: 17 Oct 11:40
Names Parsed: 17 Oct 11:35
New Models Stored: 17 Oct 11:33
Indexed: 17 Oct 11:41
Completed: 17 Oct 11:43
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-17 11:33:03 -0400 by logger.rb/56815
[START] [2019-10-17 11:33:03] logged process
[START] [2019-10-17 11:33:03] create_harvest_instance
[STOP] [2019-10-17 11:33:04] create_harvest_instance
[START] [2019-10-17 11:33:04] fetch_files
[STOP] [2019-10-17 11:33:04] fetch_files
[START] [2019-10-17 11:33:04] validate_each_file
[STOP] [2019-10-17 11:33:05] validate_each_file
[START] [2019-10-17 11:33:05] convert_to_csv
[CMD] [2019-10-17 11:33:05] /usr/bin/sort /app/public/converted_csv/zambia_sp_list_refs_17753.csv > /app/public/converted_csv/zambia_sp_list_refs_17753.csv_sorted
[CMD] [2019-10-17 11:33:05] /usr/bin/sort /app/public/converted_csv/zambia_sp_list_nodes_17754.csv > /app/public/converted_csv/zambia_sp_list_nodes_17754.csv_sorted
[CMD] [2019-10-17 11:33:05] /usr/bin/sort /app/public/converted_csv/zambia_sp_list_occurrences_17755.csv > /app/public/converted_csv/zambia_sp_list_occurrences_17755.csv_sorted
[CMD] [2019-10-17 11:33:05] /usr/bin/sort /app/public/converted_csv/zambia_sp_list_measurements_17756.csv > /app/public/converted_csv/zambia_sp_list_measurements_17756.csv_sorted
[STOP] [2019-10-17 11:33:06] convert_to_csv
[START] [2019-10-17 11:33:06] calculate_delta
[CMD] [2019-10-17 11:33:06] echo "0a" > /app/public/diff/zambia_sp_list_refs_17753.diff
[CMD] [2019-10-17 11:33:06] tail -n +1 /app/public/converted_csv/zambia_sp_list_refs_17753.csv >> /app/public/diff/zambia_sp_list_refs_17753.diff
[CMD] [2019-10-17 11:33:06] echo "." >> /app/public/diff/zambia_sp_list_refs_17753.diff
[CMD] [2019-10-17 11:33:06] echo "0a" > /app/public/diff/zambia_sp_list_nodes_17754.diff
[CMD] [2019-10-17 11:33:06] tail -n +1 /app/public/converted_csv/zambia_sp_list_nodes_17754.csv >> /app/public/diff/zambia_sp_list_nodes_17754.diff
[CMD] [2019-10-17 11:33:06] echo "." >> /app/public/diff/zambia_sp_list_nodes_17754.diff
[CMD] [2019-10-17 11:33:06] echo "0a" > /app/public/diff/zambia_sp_list_occurrences_17755.diff
[CMD] [2019-10-17 11:33:06] tail -n +1 /app/public/converted_csv/zambia_sp_list_occurrences_17755.csv >> /app/public/diff/zambia_sp_list_occurrences_17755.diff
[CMD] [2019-10-17 11:33:06] echo "." >> /app/public/diff/zambia_sp_list_occurrences_17755.diff
[CMD] [2019-10-17 11:33:06] echo "0a" > /app/public/diff/zambia_sp_list_measurements_17756.diff
[CMD] [2019-10-17 11:33:06] tail -n +1 /app/public/converted_csv/zambia_sp_list_measurements_17756.csv >> /app/public/diff/zambia_sp_list_measurements_17756.diff
[CMD] [2019-10-17 11:33:06] echo "." >> /app/public/diff/zambia_sp_list_measurements_17756.diff
[STOP] [2019-10-17 11:33:07] calculate_delta
[START] [2019-10-17 11:33:07] parse_diff_and_store
[INFO] [2019-10-17 11:33:07] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-17 11:33:07] Loading nodes diff file into memory (true lines)...
[WARN] [2019-10-17 11:33:08] Filtered Scientific Name `Hymenoptera Jakob"` to `Hymenoptera Jakob`
[INFO] [2019-10-17 11:33:10] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-17 11:33:11] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-17 11:33:46] Storing 2 References
[INFO] [2019-10-17 11:33:46] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-17 11:33:46] Average Time: 0.0
[INFO] [2019-10-17 11:33:46] Total Time: 1s
[INFO] [2019-10-17 11:33:46] Storing 9403 ScientificNames
[INFO] [2019-10-17 11:33:46] Processing group of 9403 in 10 groups of 1000
[INFO] [2019-10-17 11:33:49] Average Time: 0.333
[INFO] [2019-10-17 11:33:49] Total Time: 4s
[INFO] [2019-10-17 11:33:49] last 3 / first 3: 0.78
[INFO] [2019-10-17 11:33:49] Std.Dev: 0.07745966692414834; Max: 0.43
[INFO] [2019-10-17 11:33:49] Storing 9403 Nodes
[INFO] [2019-10-17 11:33:49] Processing group of 9403 in 10 groups of 1000
[INFO] [2019-10-17 11:33:52] Average Time: 0.269
[INFO] [2019-10-17 11:33:52] Total Time: 3s
[INFO] [2019-10-17 11:33:52] last 3 / first 3: 0.81
[INFO] [2019-10-17 11:33:52] Std.Dev: 0.05477225575051661; Max: 0.32
[INFO] [2019-10-17 11:33:52] Storing 6266 Occurrences
[INFO] [2019-10-17 11:33:52] Processing group of 6266 in 7 groups of 1000
[INFO] [2019-10-17 11:33:53] Average Time: 0.086
[INFO] [2019-10-17 11:33:53] Total Time: 1s
[INFO] [2019-10-17 11:33:53] last 3 / first 3: 0.76
[INFO] [2019-10-17 11:33:53] Std.Dev: 0.03162277660168379; Max: 0.11
[INFO] [2019-10-17 11:33:53] Storing 12540 TraitsReferences
[INFO] [2019-10-17 11:33:53] Processing group of 12540 in 13 groups of 1000
[INFO] [2019-10-17 11:33:54] Average Time: 0.073
[INFO] [2019-10-17 11:33:54] Total Time: 2s
[INFO] [2019-10-17 11:33:54] last 3 / first 3: 0.72
[INFO] [2019-10-17 11:33:54] Std.Dev: 0.03162277660168379; Max: 0.12
[INFO] [2019-10-17 11:33:54] Storing 12539 Traits
[INFO] [2019-10-17 11:33:54] Processing group of 12539 in 13 groups of 1000
[INFO] [2019-10-17 11:33:58] Average Time: 0.303
[INFO] [2019-10-17 11:33:58] Total Time: 5s
[INFO] [2019-10-17 11:33:58] last 3 / first 3: 0.93
[INFO] [2019-10-17 11:33:58] Std.Dev: 0.05477225575051661; Max: 0.43
[INFO] [2019-10-17 11:33:58] Storing 12535 MetaTraits
[INFO] [2019-10-17 11:33:58] Processing group of 12535 in 13 groups of 1000
[INFO] [2019-10-17 11:33:59] Average Time: 0.131
[INFO] [2019-10-17 11:33:59] Total Time: 2s
[INFO] [2019-10-17 11:33:59] last 3 / first 3: 0.4
[INFO] [2019-10-17 11:33:59] Std.Dev: 0.07745966692414834; Max: 0.38
[STOP] [2019-10-17 11:33:59] parse_diff_and_store
[START] [2019-10-17 11:33:59] resolve_keys
[INFO] [2019-10-17 11:34:38] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-17 11:34:42] traits to occurrences...
[INFO] [2019-10-17 11:34:47] traits to nodes (through occurrences)...
[INFO] [2019-10-17 11:34:47] Traits to sex term...
[INFO] [2019-10-17 11:34:51] Traits to lifestage term...
[INFO] [2019-10-17 11:34:55] MetaTraits to traits...
[INFO] [2019-10-17 11:34:56] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-17 11:34:57] Assocs to occurrences...
[INFO] [2019-10-17 11:34:57] Assocs to nodes...
[INFO] [2019-10-17 11:34:57] Assoc to sex term...
[INFO] [2019-10-17 11:34:57] Assoc to lifestage term...
[STOP] [2019-10-17 11:34:57] resolve_keys
[START] [2019-10-17 11:34:57] hold_for_later_1
[STOP] [2019-10-17 11:34:57] hold_for_later_1
[START] [2019-10-17 11:34:57] hold_for_later_2
[STOP] [2019-10-17 11:34:57] hold_for_later_2
[START] [2019-10-17 11:34:57] resolve_missing_parents
[STOP] [2019-10-17 11:35:16] resolve_missing_parents
[START] [2019-10-17 11:35:16] rebuild_nodes
[START] [2019-10-17 11:35:16] Flattener#flatten
[START] [2019-10-17 11:35:16] Flattener#study_resource
[START] [2019-10-17 11:35:16] Flattener#build_ancestry
[STOP] [2019-10-17 11:35:17] Flattener#build_ancestry
[INFO] [2019-10-17 11:35:17] 9403 ancestry keys
[START] [2019-10-17 11:35:17] build_node_ancestors
[INFO] [2019-10-17 11:35:17] old ancestors deleted.
[STOP] [2019-10-17 11:35:19] build_node_ancestors
[START] [2019-10-17 11:35:21] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:35:21] Flattener#propagate_ancestor_ids
[STOP] [2019-10-17 11:35:21] Flattener#flatten
[STOP] [2019-10-17 11:35:21] rebuild_nodes
[START] [2019-10-17 11:35:21] resolve_missing_media_owners
[STOP] [2019-10-17 11:35:21] resolve_missing_media_owners
[START] [2019-10-17 11:35:21] sanitize_media_verbatims
[STOP] [2019-10-17 11:35:21] sanitize_media_verbatims
[START] [2019-10-17 11:35:21] queue_downloads
[STOP] [2019-10-17 11:35:21] queue_downloads
[START] [2019-10-17 11:35:21] parse_names
[WARN] [2019-10-17 11:35:21] I see 9403 names which still need to be parsed.
[STOP] [2019-10-17 11:35:29] parse_names
[START] [2019-10-17 11:35:29] denormalize_canonical_names_to_nodes
[STOP] [2019-10-17 11:35:29] denormalize_canonical_names_to_nodes
[START] [2019-10-17 11:35:29] match_nodes
[START] [2019-10-17 11:35:29] map_all_nodes_to_pages
[STOP] [2019-10-17 11:40:42] map_all_nodes_to_pages
[INFO] [2019-10-17 11:40:42] 422 Unmatched nodes (of 9403)! That's too many to output. First 10: Hirundo abyssinica (#52727624); Hirundo cucullata (#52729672); Hirundo fuligula (#52730574); Hirundo semirufa (#52731604); Hirundo senegalensis (#52733217); Delichon urbica (#52732237); Euplectes macrourus (#52728234); Ortygospiza fuscocrissa (#52728467); Ortygospiza gabonensis (#52730866); Andropadus virens (#52728021)
[START] [2019-10-17 11:40:42] update_nodes
[STOP] [2019-10-17 11:40:45] update_nodes
[STOP] [2019-10-17 11:40:45] match_nodes
[START] [2019-10-17 11:40:46] reindex_search
[STOP] [2019-10-17 11:41:01] reindex_search
[START] [2019-10-17 11:41:01] normalize_units
[STOP] [2019-10-17 11:41:01] normalize_units
[START] [2019-10-17 11:41:01] calculate_statistics
[STOP] [2019-10-17 11:41:01] calculate_statistics
[START] [2019-10-17 11:41:01] complete_harvest_instance
[START] [2019-10-17 11:41:01] overall_tsv_creation
[INFO] [2019-10-17 11:41:01] Processing group of 9403 in 1 batches of 10000
[INFO] [2019-10-17 11:42:27] 6266 Traits (unfiltered)...
[INFO] [2019-10-17 11:42:40] 6266 Traits (filtered)...
[INFO] [2019-10-17 11:42:40] 0 Associations (filtered)...
[INFO] [2019-10-17 11:43:29] 31325 metadata added.
[INFO] [2019-10-17 11:43:29] 0 metadata added.
[INFO] [2019-10-17 11:43:29] Average Time: 118.13
[INFO] [2019-10-17 11:43:29] Total Time: 2m29s
[STOP] [2019-10-17 11:43:29] overall_tsv_creation
[INFO] [2019-10-17 11:43:29] Done. Check your files:
[INFO] [2019-10-17 11:43:29] (9403 lines) /app/public/data/zambia_sp_list/publish_nodes.tsv
[INFO] [2019-10-17 11:43:29] (27457 lines) /app/public/data/zambia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-17 11:43:30] (9403 lines) /app/public/data/zambia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-17 11:43:30] (6267 lines) /app/public/data/zambia_sp_list/publish_traits.tsv
[INFO] [2019-10-17 11:43:30] (31326 lines) /app/public/data/zambia_sp_list/publish_metadata.tsv
[STOP] [2019-10-17 11:43:30] complete_harvest_instance
[START] [2019-10-17 11:43:30] completed
[STOP] [2019-10-17 11:43:30] completed
[STOP] [2019-10-17 11:43:30] logged process, took 626.58

Latest Process