Harvest for Tanzania Species List Created 16 Oct 11:21

Stage: completed
Fetched: 16 Oct 11:21
Validated: 16 Oct 11:21
Deltas Created 16 Oct 11:21
Units Normalized: 16 Oct 11:55
Ancestry Built: 16 Oct 11:26
Nodes Matched: 16 Oct 11:53
Names Parsed: 16 Oct 11:27
New Models Stored: 16 Oct 11:23
Indexed: 16 Oct 11:55
Completed: 16 Oct 12:02
Time to Harvest: 1 minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-16 11:21:04 -0400 by logger.rb/56815
[START] [2019-10-16 11:21:04] logged process
[START] [2019-10-16 11:21:04] create_harvest_instance
[STOP] [2019-10-16 11:21:05] create_harvest_instance
[START] [2019-10-16 11:21:05] fetch_files
[STOP] [2019-10-16 11:21:05] fetch_files
[START] [2019-10-16 11:21:05] validate_each_file
[STOP] [2019-10-16 11:21:08] validate_each_file
[START] [2019-10-16 11:21:08] convert_to_csv
[CMD] [2019-10-16 11:21:08] /usr/bin/sort /app/public/converted_csv/tanzania_sp_list_refs_17401.csv > /app/public/converted_csv/tanzania_sp_list_refs_17401.csv_sorted
[CMD] [2019-10-16 11:21:08] /usr/bin/sort /app/public/converted_csv/tanzania_sp_list_nodes_17402.csv > /app/public/converted_csv/tanzania_sp_list_nodes_17402.csv_sorted
[CMD] [2019-10-16 11:21:09] /usr/bin/sort /app/public/converted_csv/tanzania_sp_list_occurrences_17403.csv > /app/public/converted_csv/tanzania_sp_list_occurrences_17403.csv_sorted
[CMD] [2019-10-16 11:21:09] /usr/bin/sort /app/public/converted_csv/tanzania_sp_list_measurements_17404.csv > /app/public/converted_csv/tanzania_sp_list_measurements_17404.csv_sorted
[STOP] [2019-10-16 11:21:09] convert_to_csv
[START] [2019-10-16 11:21:09] calculate_delta
[CMD] [2019-10-16 11:21:09] echo "0a" > /app/public/diff/tanzania_sp_list_refs_17401.diff
[CMD] [2019-10-16 11:21:10] tail -n +1 /app/public/converted_csv/tanzania_sp_list_refs_17401.csv >> /app/public/diff/tanzania_sp_list_refs_17401.diff
[CMD] [2019-10-16 11:21:10] echo "." >> /app/public/diff/tanzania_sp_list_refs_17401.diff
[CMD] [2019-10-16 11:21:10] echo "0a" > /app/public/diff/tanzania_sp_list_nodes_17402.diff
[CMD] [2019-10-16 11:21:10] tail -n +1 /app/public/converted_csv/tanzania_sp_list_nodes_17402.csv >> /app/public/diff/tanzania_sp_list_nodes_17402.diff
[CMD] [2019-10-16 11:21:11] echo "." >> /app/public/diff/tanzania_sp_list_nodes_17402.diff
[CMD] [2019-10-16 11:21:11] echo "0a" > /app/public/diff/tanzania_sp_list_occurrences_17403.diff
[CMD] [2019-10-16 11:21:11] tail -n +1 /app/public/converted_csv/tanzania_sp_list_occurrences_17403.csv >> /app/public/diff/tanzania_sp_list_occurrences_17403.diff
[CMD] [2019-10-16 11:21:11] echo "." >> /app/public/diff/tanzania_sp_list_occurrences_17403.diff
[CMD] [2019-10-16 11:21:12] echo "0a" > /app/public/diff/tanzania_sp_list_measurements_17404.diff
[CMD] [2019-10-16 11:21:12] tail -n +1 /app/public/converted_csv/tanzania_sp_list_measurements_17404.csv >> /app/public/diff/tanzania_sp_list_measurements_17404.diff
[CMD] [2019-10-16 11:21:12] echo "." >> /app/public/diff/tanzania_sp_list_measurements_17404.diff
[STOP] [2019-10-16 11:21:13] calculate_delta
[START] [2019-10-16 11:21:13] parse_diff_and_store
[INFO] [2019-10-16 11:21:13] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 11:21:13] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 11:21:23] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 11:21:26] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 11:23:14] Storing 2 References
[INFO] [2019-10-16 11:23:14] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 11:23:14] Average Time: 0.0
[INFO] [2019-10-16 11:23:14] Total Time: 1s
[INFO] [2019-10-16 11:23:14] Storing 25233 ScientificNames
[INFO] [2019-10-16 11:23:14] Processing group of 25233 in 26 groups of 1000
[INFO] [2019-10-16 11:23:23] Average Time: 0.345
[INFO] [2019-10-16 11:23:23] Total Time: 10s
[INFO] [2019-10-16 11:23:23] last 3 / first 3: 0.72
[INFO] [2019-10-16 11:23:23] Std.Dev: 0.05477225575051661; Max: 0.42
[INFO] [2019-10-16 11:23:23] Storing 25233 Nodes
[INFO] [2019-10-16 11:23:23] Processing group of 25233 in 26 groups of 1000
[INFO] [2019-10-16 11:23:31] Average Time: 0.316
[INFO] [2019-10-16 11:23:31] Total Time: 9s
[INFO] [2019-10-16 11:23:31] last 3 / first 3: 1.15
[INFO] [2019-10-16 11:23:31] Std.Dev: 0.044721359549995794; Max: 0.49
[INFO] [2019-10-16 11:23:31] Storing 18316 Occurrences
[INFO] [2019-10-16 11:23:31] Processing group of 18316 in 19 groups of 1000
[INFO] [2019-10-16 11:23:34] Average Time: 0.152
[INFO] [2019-10-16 11:23:34] Total Time: 3s
[INFO] [2019-10-16 11:23:34] last 3 / first 3: 0.45
[INFO] [2019-10-16 11:23:34] Std.Dev: 0.08944271909999159; Max: 0.43
[INFO] [2019-10-16 11:23:34] Storing 36750 TraitsReferences
[INFO] [2019-10-16 11:23:34] Processing group of 36750 in 37 groups of 1000
[INFO] [2019-10-16 11:23:37] Average Time: 0.072
[INFO] [2019-10-16 11:23:37] Total Time: 3s
[INFO] [2019-10-16 11:23:37] last 3 / first 3: 0.89
[INFO] [2019-10-16 11:23:37] Std.Dev: 0.0; Max: 0.15
[INFO] [2019-10-16 11:23:37] Storing 36749 Traits
[INFO] [2019-10-16 11:23:37] Processing group of 36749 in 37 groups of 1000
[INFO] [2019-10-16 11:23:48] Average Time: 0.291
[INFO] [2019-10-16 11:23:48] Total Time: 11s
[INFO] [2019-10-16 11:23:48] last 3 / first 3: 0.91
[INFO] [2019-10-16 11:23:48] Std.Dev: 0.03162277660168379; Max: 0.41
[INFO] [2019-10-16 11:23:48] Storing 36721 MetaTraits
[INFO] [2019-10-16 11:23:48] Processing group of 36721 in 37 groups of 1000
[INFO] [2019-10-16 11:23:52] Average Time: 0.109
[INFO] [2019-10-16 11:23:52] Total Time: 5s
[INFO] [2019-10-16 11:23:52] last 3 / first 3: 0.85
[INFO] [2019-10-16 11:23:52] Std.Dev: 0.0; Max: 0.2
[STOP] [2019-10-16 11:23:52] parse_diff_and_store
[START] [2019-10-16 11:23:52] resolve_keys
[INFO] [2019-10-16 11:25:12] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 11:25:19] traits to occurrences...
[INFO] [2019-10-16 11:25:28] traits to nodes (through occurrences)...
[INFO] [2019-10-16 11:25:28] Traits to sex term...
[INFO] [2019-10-16 11:25:36] Traits to lifestage term...
[INFO] [2019-10-16 11:25:45] MetaTraits to traits...
[INFO] [2019-10-16 11:25:47] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 11:25:52] Assocs to occurrences...
[INFO] [2019-10-16 11:25:52] Assocs to nodes...
[INFO] [2019-10-16 11:25:52] Assoc to sex term...
[INFO] [2019-10-16 11:25:52] Assoc to lifestage term...
[STOP] [2019-10-16 11:25:52] resolve_keys
[START] [2019-10-16 11:25:52] hold_for_later_1
[STOP] [2019-10-16 11:25:52] hold_for_later_1
[START] [2019-10-16 11:25:52] hold_for_later_2
[STOP] [2019-10-16 11:25:52] hold_for_later_2
[START] [2019-10-16 11:25:52] resolve_missing_parents
[STOP] [2019-10-16 11:26:37] resolve_missing_parents
[START] [2019-10-16 11:26:37] rebuild_nodes
[START] [2019-10-16 11:26:37] Flattener#flatten
[START] [2019-10-16 11:26:37] Flattener#study_resource
[START] [2019-10-16 11:26:37] Flattener#build_ancestry
[STOP] [2019-10-16 11:26:40] Flattener#build_ancestry
[INFO] [2019-10-16 11:26:40] 25233 ancestry keys
[START] [2019-10-16 11:26:40] build_node_ancestors
[INFO] [2019-10-16 11:26:40] old ancestors deleted.
[STOP] [2019-10-16 11:26:47] build_node_ancestors
[START] [2019-10-16 11:26:54] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 11:26:57] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 11:26:57] Flattener#flatten
[STOP] [2019-10-16 11:26:57] rebuild_nodes
[START] [2019-10-16 11:26:57] resolve_missing_media_owners
[STOP] [2019-10-16 11:26:57] resolve_missing_media_owners
[START] [2019-10-16 11:26:57] sanitize_media_verbatims
[STOP] [2019-10-16 11:26:57] sanitize_media_verbatims
[START] [2019-10-16 11:26:57] queue_downloads
[STOP] [2019-10-16 11:26:57] queue_downloads
[START] [2019-10-16 11:26:57] parse_names
[WARN] [2019-10-16 11:26:57] I see 25233 names which still need to be parsed.
[STOP] [2019-10-16 11:27:16] parse_names
[START] [2019-10-16 11:27:16] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 11:27:16] denormalize_canonical_names_to_nodes
[START] [2019-10-16 11:27:17] match_nodes
[START] [2019-10-16 11:27:17] map_all_nodes_to_pages
[STOP] [2019-10-16 11:53:50] map_all_nodes_to_pages
[INFO] [2019-10-16 11:53:50] 1662 Unmatched nodes (of 25233)! That's too many to output. First 10: Schistosoma (#52341677); Schistosoma mansoni (#52341676); Schistosoma haematobium (#52341936); Diplostomida (#52341679); Mansonia uniformis (#52359322); Ceratitis querita (#52356933); Bactrocera curcubitae (#52347334); Bactrocera adustus (#52350642); Clinotaenia superba (#52363609); Richardidae (#52347335)
[START] [2019-10-16 11:53:50] update_nodes
[STOP] [2019-10-16 11:53:59] update_nodes
[STOP] [2019-10-16 11:53:59] match_nodes
[START] [2019-10-16 11:53:59] reindex_search
[STOP] [2019-10-16 11:55:24] reindex_search
[START] [2019-10-16 11:55:24] normalize_units
[STOP] [2019-10-16 11:55:24] normalize_units
[START] [2019-10-16 11:55:24] calculate_statistics
[STOP] [2019-10-16 11:55:24] calculate_statistics
[START] [2019-10-16 11:55:24] complete_harvest_instance
[START] [2019-10-16 11:55:24] overall_tsv_creation
[INFO] [2019-10-16 11:55:24] Processing group of 25233 in 3 batches of 10000
[INFO] [2019-10-16 11:56:54] 6678 Traits (unfiltered)...
[INFO] [2019-10-16 11:57:08] 6678 Traits (filtered)...
[INFO] [2019-10-16 11:57:08] 0 Associations (filtered)...
[INFO] [2019-10-16 11:57:58] 33387 metadata added.
[INFO] [2019-10-16 11:57:58] 0 metadata added.
[INFO] [2019-10-16 11:59:30] 7601 Traits (unfiltered)...
[INFO] [2019-10-16 11:59:43] 7601 Traits (filtered)...
[INFO] [2019-10-16 11:59:43] 0 Associations (filtered)...
[INFO] [2019-10-16 12:00:41] 37994 metadata added.
[INFO] [2019-10-16 12:00:41] 0 metadata added.
[INFO] [2019-10-16 12:01:51] 4037 Traits (unfiltered)...
[INFO] [2019-10-16 12:02:05] 4037 Traits (filtered)...
[INFO] [2019-10-16 12:02:05] 0 Associations (filtered)...
[INFO] [2019-10-16 12:02:51] 20171 metadata added.
[INFO] [2019-10-16 12:02:51] 0 metadata added.
[INFO] [2019-10-16 12:02:51] Average Time: 122.543
[INFO] [2019-10-16 12:02:51] Total Time: 7m27s
[STOP] [2019-10-16 12:02:51] overall_tsv_creation
[INFO] [2019-10-16 12:02:51] Done. Check your files:
[INFO] [2019-10-16 12:02:51] (25233 lines) /app/public/data/tanzania_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 12:02:51] (95493 lines) /app/public/data/tanzania_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 12:02:51] (25233 lines) /app/public/data/tanzania_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 12:02:52] (18317 lines) /app/public/data/tanzania_sp_list/publish_traits.tsv
[INFO] [2019-10-16 12:02:52] (91553 lines) /app/public/data/tanzania_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 12:02:52] complete_harvest_instance
[START] [2019-10-16 12:02:52] completed
[STOP] [2019-10-16 12:02:52] completed
[STOP] [2019-10-16 12:02:52] logged process, took 2507.88

Latest Process