Harvest for Afghanistan Species List Created 30 Jul 08:57

Stage: completed
Fetched: 30 Jul 08:57
Validated: 30 Jul 08:57
Deltas Created 30 Jul 08:57
Units Normalized: 30 Jul 09:01
Ancestry Built: 30 Jul 08:59
Nodes Matched: 30 Jul 09:01
Names Parsed: 30 Jul 08:59
New Models Stored: 30 Jul 08:58
Indexed: 30 Jul 09:01
Completed: 30 Jul 09:03
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-07-30 08:57:40 -0400 by logger.rb/56815
[START] [2019-07-30 08:57:40] logged process
[START] [2019-07-30 08:57:40] create_harvest_instance
[STOP] [2019-07-30 08:57:40] create_harvest_instance
[START] [2019-07-30 08:57:40] fetch_files
[STOP] [2019-07-30 08:57:40] fetch_files
[START] [2019-07-30 08:57:40] validate_each_file
[STOP] [2019-07-30 08:57:41] validate_each_file
[START] [2019-07-30 08:57:41] convert_to_csv
[CMD] [2019-07-30 08:57:41] /usr/bin/sort /app/public/converted_csv/afghanistan_sp_l_refs_14333.csv > /app/public/converted_csv/afghanistan_sp_l_refs_14333.csv_sorted
[CMD] [2019-07-30 08:57:41] /usr/bin/sort /app/public/converted_csv/afghanistan_sp_l_nodes_14334.csv > /app/public/converted_csv/afghanistan_sp_l_nodes_14334.csv_sorted
[CMD] [2019-07-30 08:57:41] /usr/bin/sort /app/public/converted_csv/afghanistan_sp_l_occurrences_14335.csv > /app/public/converted_csv/afghanistan_sp_l_occurrences_14335.csv_sorted
[CMD] [2019-07-30 08:57:41] /usr/bin/sort /app/public/converted_csv/afghanistan_sp_l_measurements_14336.csv > /app/public/converted_csv/afghanistan_sp_l_measurements_14336.csv_sorted
[STOP] [2019-07-30 08:57:41] convert_to_csv
[START] [2019-07-30 08:57:41] calculate_delta
[CMD] [2019-07-30 08:57:41] echo "0a" > /app/public/diff/afghanistan_sp_l_refs_14333.diff
[CMD] [2019-07-30 08:57:41] tail -n +1 /app/public/converted_csv/afghanistan_sp_l_refs_14333.csv >> /app/public/diff/afghanistan_sp_l_refs_14333.diff
[CMD] [2019-07-30 08:57:41] echo "." >> /app/public/diff/afghanistan_sp_l_refs_14333.diff
[CMD] [2019-07-30 08:57:41] echo "0a" > /app/public/diff/afghanistan_sp_l_nodes_14334.diff
[CMD] [2019-07-30 08:57:42] tail -n +1 /app/public/converted_csv/afghanistan_sp_l_nodes_14334.csv >> /app/public/diff/afghanistan_sp_l_nodes_14334.diff
[CMD] [2019-07-30 08:57:42] echo "." >> /app/public/diff/afghanistan_sp_l_nodes_14334.diff
[CMD] [2019-07-30 08:57:42] echo "0a" > /app/public/diff/afghanistan_sp_l_occurrences_14335.diff
[CMD] [2019-07-30 08:57:42] tail -n +1 /app/public/converted_csv/afghanistan_sp_l_occurrences_14335.csv >> /app/public/diff/afghanistan_sp_l_occurrences_14335.diff
[CMD] [2019-07-30 08:57:42] echo "." >> /app/public/diff/afghanistan_sp_l_occurrences_14335.diff
[CMD] [2019-07-30 08:57:42] echo "0a" > /app/public/diff/afghanistan_sp_l_measurements_14336.diff
[CMD] [2019-07-30 08:57:42] tail -n +1 /app/public/converted_csv/afghanistan_sp_l_measurements_14336.csv >> /app/public/diff/afghanistan_sp_l_measurements_14336.diff
[CMD] [2019-07-30 08:57:42] echo "." >> /app/public/diff/afghanistan_sp_l_measurements_14336.diff
[STOP] [2019-07-30 08:57:42] calculate_delta
[START] [2019-07-30 08:57:42] parse_diff_and_store
[INFO] [2019-07-30 08:57:42] Loading refs diff file into memory (true lines)...
[INFO] [2019-07-30 08:57:42] Loading nodes diff file into memory (true lines)...
[INFO] [2019-07-30 08:57:44] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-07-30 08:57:44] Loading measurements diff file into memory (true lines)...
[INFO] [2019-07-30 08:58:08] Storing 2 References
[INFO] [2019-07-30 08:58:08] Processing group of 2 in 1 groups of 1000
[INFO] [2019-07-30 08:58:08] Average Time: 0.0
[INFO] [2019-07-30 08:58:08] Total Time: 1s
[INFO] [2019-07-30 08:58:08] Storing 6184 ScientificNames
[INFO] [2019-07-30 08:58:08] Processing group of 6184 in 7 groups of 1000
[INFO] [2019-07-30 08:58:10] Average Time: 0.3
[INFO] [2019-07-30 08:58:10] Total Time: 3s
[INFO] [2019-07-30 08:58:10] last 3 / first 3: 0.73
[INFO] [2019-07-30 08:58:10] Std.Dev: 0.11401754250991379; Max: 0.39
[INFO] [2019-07-30 08:58:10] Storing 6184 Nodes
[INFO] [2019-07-30 08:58:10] Processing group of 6184 in 7 groups of 1000
[INFO] [2019-07-30 08:58:12] Average Time: 0.249
[INFO] [2019-07-30 08:58:12] Total Time: 2s
[INFO] [2019-07-30 08:58:12] last 3 / first 3: 0.83
[INFO] [2019-07-30 08:58:12] Std.Dev: 0.09486832980505137; Max: 0.35
[INFO] [2019-07-30 08:58:12] Storing 3856 Occurrences
[INFO] [2019-07-30 08:58:12] Processing group of 3856 in 4 groups of 1000
[INFO] [2019-07-30 08:58:13] Average Time: 0.095
[INFO] [2019-07-30 08:58:13] Total Time: 1s
[INFO] [2019-07-30 08:58:13] Storing 8244 TraitsReferences
[INFO] [2019-07-30 08:58:13] Processing group of 8244 in 9 groups of 1000
[INFO] [2019-07-30 08:58:13] Average Time: 0.069
[INFO] [2019-07-30 08:58:13] Total Time: 1s
[INFO] [2019-07-30 08:58:13] last 3 / first 3: 0.5
[INFO] [2019-07-30 08:58:13] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-07-30 08:58:13] Storing 8243 Traits
[INFO] [2019-07-30 08:58:13] Processing group of 8243 in 9 groups of 1000
[INFO] [2019-07-30 08:58:16] Average Time: 0.302
[INFO] [2019-07-30 08:58:16] Total Time: 3s
[INFO] [2019-07-30 08:58:16] last 3 / first 3: 0.67
[INFO] [2019-07-30 08:58:16] Std.Dev: 0.1; Max: 0.45
[INFO] [2019-07-30 08:58:16] Storing 8244 MetaTraits
[INFO] [2019-07-30 08:58:16] Processing group of 8244 in 9 groups of 1000
[INFO] [2019-07-30 08:58:17] Average Time: 0.124
[INFO] [2019-07-30 08:58:17] Total Time: 2s
[INFO] [2019-07-30 08:58:17] last 3 / first 3: 0.64
[INFO] [2019-07-30 08:58:17] Std.Dev: 0.03162277660168379; Max: 0.16
[STOP] [2019-07-30 08:58:17] parse_diff_and_store
[START] [2019-07-30 08:58:17] resolve_keys
[INFO] [2019-07-30 08:58:43] Occurrences to nodes (through scientific_names)...
[INFO] [2019-07-30 08:58:45] traits to occurrences...
[INFO] [2019-07-30 08:58:47] traits to nodes (through occurrences)...
[INFO] [2019-07-30 08:58:47] Traits to sex term...
[INFO] [2019-07-30 08:58:48] Traits to lifestage term...
[INFO] [2019-07-30 08:58:50] MetaTraits to traits...
[INFO] [2019-07-30 08:58:51] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-07-30 08:58:52] Assocs to occurrences...
[INFO] [2019-07-30 08:58:52] Assocs to nodes...
[INFO] [2019-07-30 08:58:52] Assoc to sex term...
[INFO] [2019-07-30 08:58:52] Assoc to lifestage term...
[STOP] [2019-07-30 08:58:52] resolve_keys
[START] [2019-07-30 08:58:52] hold_for_later_1
[STOP] [2019-07-30 08:58:52] hold_for_later_1
[START] [2019-07-30 08:58:52] hold_for_later_2
[STOP] [2019-07-30 08:58:52] hold_for_later_2
[START] [2019-07-30 08:58:52] resolve_missing_parents
[STOP] [2019-07-30 08:59:04] resolve_missing_parents
[START] [2019-07-30 08:59:04] rebuild_nodes
[START] [2019-07-30 08:59:04] Flattener#flatten
[START] [2019-07-30 08:59:04] Flattener#study_resource
[START] [2019-07-30 08:59:04] Flattener#build_ancestry
[STOP] [2019-07-30 08:59:05] Flattener#build_ancestry
[INFO] [2019-07-30 08:59:05] 6184 ancestry keys
[START] [2019-07-30 08:59:05] build_node_ancestors
[INFO] [2019-07-30 08:59:05] old ancestors deleted.
[STOP] [2019-07-30 08:59:06] build_node_ancestors
[START] [2019-07-30 08:59:07] Flattener#propagate_ancestor_ids
[STOP] [2019-07-30 08:59:07] Flattener#propagate_ancestor_ids
[STOP] [2019-07-30 08:59:07] Flattener#flatten
[STOP] [2019-07-30 08:59:07] rebuild_nodes
[START] [2019-07-30 08:59:07] resolve_missing_media_owners
[STOP] [2019-07-30 08:59:07] resolve_missing_media_owners
[START] [2019-07-30 08:59:07] sanitize_media_verbatims
[STOP] [2019-07-30 08:59:07] sanitize_media_verbatims
[START] [2019-07-30 08:59:07] queue_downloads
[STOP] [2019-07-30 08:59:07] queue_downloads
[START] [2019-07-30 08:59:07] parse_names
[WARN] [2019-07-30 08:59:07] I see 6184 names which still need to be parsed.
[STOP] [2019-07-30 08:59:13] parse_names
[START] [2019-07-30 08:59:13] denormalize_canonical_names_to_nodes
[STOP] [2019-07-30 08:59:13] denormalize_canonical_names_to_nodes
[START] [2019-07-30 08:59:13] match_nodes
[START] [2019-07-30 08:59:13] map_all_nodes_to_pages
[STOP] [2019-07-30 09:01:05] map_all_nodes_to_pages
[INFO] [2019-07-30 09:01:05] 445 Unmatched nodes (of 6184)! That's too many to output. First 10: Streptopelia senegalensis (#44597662); Calandrella rufescens (#44598450); Delichon urbica (#44603800); Sturnus pagodarum (#44602546); Oenanthe alboniger (#44602382); Phoenicurus erythronota (#44602867); Erythropygia (#44599067); Erythropygia galactotes (#44599066); Sylvia margelanica (#44602415); Garrulax lineatus (#44603207)
[START] [2019-07-30 09:01:05] update_nodes
[STOP] [2019-07-30 09:01:07] update_nodes
[STOP] [2019-07-30 09:01:07] match_nodes
[START] [2019-07-30 09:01:07] reindex_search
[STOP] [2019-07-30 09:01:16] reindex_search
[START] [2019-07-30 09:01:16] normalize_units
[STOP] [2019-07-30 09:01:16] normalize_units
[START] [2019-07-30 09:01:16] calculate_statistics
[STOP] [2019-07-30 09:01:16] calculate_statistics
[START] [2019-07-30 09:01:16] complete_harvest_instance
[START] [2019-07-30 09:01:16] overall_tsv_creation
[INFO] [2019-07-30 09:01:16] Processing group of 6184 in 1 batches of 10000
[INFO] [2019-07-30 09:02:38] 3856 Traits (unfiltered)...
[INFO] [2019-07-30 09:02:53] 3856 Traits (filtered)...
[INFO] [2019-07-30 09:02:53] 0 Associations (filtered)...
[INFO] [2019-07-30 09:03:44] 19280 metadata added.
[INFO] [2019-07-30 09:03:44] 0 metadata added.
[INFO] [2019-07-30 09:03:44] Average Time: 113.01
[INFO] [2019-07-30 09:03:44] Total Time: 2m29s
[STOP] [2019-07-30 09:03:44] overall_tsv_creation
[INFO] [2019-07-30 09:03:44] Done. Check your files:
[INFO] [2019-07-30 09:03:44] (6184 lines) /app/public/data/afghanistan_sp_l/publish_nodes.tsv
[INFO] [2019-07-30 09:03:44] (15304 lines) /app/public/data/afghanistan_sp_l/publish_node_ancestors.tsv
[INFO] [2019-07-30 09:03:44] (6184 lines) /app/public/data/afghanistan_sp_l/publish_scientific_names.tsv
[INFO] [2019-07-30 09:03:44] (3857 lines) /app/public/data/afghanistan_sp_l/publish_traits.tsv
[INFO] [2019-07-30 09:03:44] (19281 lines) /app/public/data/afghanistan_sp_l/publish_metadata.tsv
[STOP] [2019-07-30 09:03:44] complete_harvest_instance
[START] [2019-07-30 09:03:44] completed
[STOP] [2019-07-30 09:03:44] completed
[STOP] [2019-07-30 09:03:44] logged process, took 364.55

Latest Process