Harvest for Burkina Faso Species List Created 11 Oct 23:24

Stage: completed
Fetched: 11 Oct 23:24
Validated: 11 Oct 23:24
Deltas Created 11 Oct 23:24
Units Normalized: 11 Oct 23:28
Ancestry Built: 11 Oct 23:25
Nodes Matched: 11 Oct 23:28
Names Parsed: 11 Oct 23:25
New Models Stored: 11 Oct 23:24
Indexed: 11 Oct 23:28
Completed: 11 Oct 23:30
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-11 23:24:09 -0400 by logger.rb/56815
[START] [2019-10-11 23:24:09] logged process
[START] [2019-10-11 23:24:09] create_harvest_instance
[STOP] [2019-10-11 23:24:09] create_harvest_instance
[START] [2019-10-11 23:24:09] fetch_files
[STOP] [2019-10-11 23:24:09] fetch_files
[START] [2019-10-11 23:24:09] validate_each_file
[STOP] [2019-10-11 23:24:10] validate_each_file
[START] [2019-10-11 23:24:10] convert_to_csv
[CMD] [2019-10-11 23:24:10] /usr/bin/sort /app/public/converted_csv/burkina_faso_sp__refs_15339.csv > /app/public/converted_csv/burkina_faso_sp__refs_15339.csv_sorted
[CMD] [2019-10-11 23:24:10] /usr/bin/sort /app/public/converted_csv/burkina_faso_sp__nodes_15340.csv > /app/public/converted_csv/burkina_faso_sp__nodes_15340.csv_sorted
[CMD] [2019-10-11 23:24:10] /usr/bin/sort /app/public/converted_csv/burkina_faso_sp__occurrences_15341.csv > /app/public/converted_csv/burkina_faso_sp__occurrences_15341.csv_sorted
[CMD] [2019-10-11 23:24:11] /usr/bin/sort /app/public/converted_csv/burkina_faso_sp__measurements_15342.csv > /app/public/converted_csv/burkina_faso_sp__measurements_15342.csv_sorted
[STOP] [2019-10-11 23:24:11] convert_to_csv
[START] [2019-10-11 23:24:11] calculate_delta
[CMD] [2019-10-11 23:24:11] echo "0a" > /app/public/diff/burkina_faso_sp__refs_15339.diff
[CMD] [2019-10-11 23:24:11] tail -n +1 /app/public/converted_csv/burkina_faso_sp__refs_15339.csv >> /app/public/diff/burkina_faso_sp__refs_15339.diff
[CMD] [2019-10-11 23:24:11] echo "." >> /app/public/diff/burkina_faso_sp__refs_15339.diff
[CMD] [2019-10-11 23:24:11] echo "0a" > /app/public/diff/burkina_faso_sp__nodes_15340.diff
[CMD] [2019-10-11 23:24:11] tail -n +1 /app/public/converted_csv/burkina_faso_sp__nodes_15340.csv >> /app/public/diff/burkina_faso_sp__nodes_15340.diff
[CMD] [2019-10-11 23:24:11] echo "." >> /app/public/diff/burkina_faso_sp__nodes_15340.diff
[CMD] [2019-10-11 23:24:11] echo "0a" > /app/public/diff/burkina_faso_sp__occurrences_15341.diff
[CMD] [2019-10-11 23:24:11] tail -n +1 /app/public/converted_csv/burkina_faso_sp__occurrences_15341.csv >> /app/public/diff/burkina_faso_sp__occurrences_15341.diff
[CMD] [2019-10-11 23:24:11] echo "." >> /app/public/diff/burkina_faso_sp__occurrences_15341.diff
[CMD] [2019-10-11 23:24:12] echo "0a" > /app/public/diff/burkina_faso_sp__measurements_15342.diff
[CMD] [2019-10-11 23:24:12] tail -n +1 /app/public/converted_csv/burkina_faso_sp__measurements_15342.csv >> /app/public/diff/burkina_faso_sp__measurements_15342.diff
[CMD] [2019-10-11 23:24:12] echo "." >> /app/public/diff/burkina_faso_sp__measurements_15342.diff
[STOP] [2019-10-11 23:24:12] calculate_delta
[START] [2019-10-11 23:24:12] parse_diff_and_store
[INFO] [2019-10-11 23:24:12] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-11 23:24:12] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-11 23:24:14] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-11 23:24:15] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-11 23:24:34] Storing 2 References
[INFO] [2019-10-11 23:24:34] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-11 23:24:34] Average Time: 0.0
[INFO] [2019-10-11 23:24:34] Total Time: 1s
[INFO] [2019-10-11 23:24:34] Storing 5184 ScientificNames
[INFO] [2019-10-11 23:24:34] Processing group of 5184 in 6 groups of 1000
[INFO] [2019-10-11 23:24:36] Average Time: 0.328
[INFO] [2019-10-11 23:24:36] Total Time: 2s
[INFO] [2019-10-11 23:24:36] Storing 5184 Nodes
[INFO] [2019-10-11 23:24:36] Processing group of 5184 in 6 groups of 1000
[INFO] [2019-10-11 23:24:38] Average Time: 0.26
[INFO] [2019-10-11 23:24:38] Total Time: 2s
[INFO] [2019-10-11 23:24:38] Storing 3374 Occurrences
[INFO] [2019-10-11 23:24:38] Processing group of 3374 in 4 groups of 1000
[INFO] [2019-10-11 23:24:38] Average Time: 0.105
[INFO] [2019-10-11 23:24:38] Total Time: 1s
[INFO] [2019-10-11 23:24:38] Storing 6820 TraitsReferences
[INFO] [2019-10-11 23:24:38] Processing group of 6820 in 7 groups of 1000
[INFO] [2019-10-11 23:24:39] Average Time: 0.083
[INFO] [2019-10-11 23:24:39] Total Time: 1s
[INFO] [2019-10-11 23:24:39] last 3 / first 3: 0.65
[INFO] [2019-10-11 23:24:39] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-10-11 23:24:39] Storing 6819 Traits
[INFO] [2019-10-11 23:24:39] Processing group of 6819 in 7 groups of 1000
[INFO] [2019-10-11 23:24:42] Average Time: 0.369
[INFO] [2019-10-11 23:24:42] Total Time: 3s
[INFO] [2019-10-11 23:24:42] last 3 / first 3: 0.9
[INFO] [2019-10-11 23:24:42] Std.Dev: 0.044721359549995794; Max: 0.44
[INFO] [2019-10-11 23:24:42] Storing 6817 MetaTraits
[INFO] [2019-10-11 23:24:42] Processing group of 6817 in 7 groups of 1000
[INFO] [2019-10-11 23:24:44] Average Time: 0.293
[INFO] [2019-10-11 23:24:44] Total Time: 3s
[INFO] [2019-10-11 23:24:44] last 3 / first 3: 0.26
[INFO] [2019-10-11 23:24:44] Std.Dev: 0.31304951684997057; Max: 0.99
[STOP] [2019-10-11 23:24:44] parse_diff_and_store
[START] [2019-10-11 23:24:44] resolve_keys
[INFO] [2019-10-11 23:25:06] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-11 23:25:08] traits to occurrences...
[INFO] [2019-10-11 23:25:12] traits to nodes (through occurrences)...
[INFO] [2019-10-11 23:25:12] Traits to sex term...
[INFO] [2019-10-11 23:25:14] Traits to lifestage term...
[INFO] [2019-10-11 23:25:16] MetaTraits to traits...
[INFO] [2019-10-11 23:25:17] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-11 23:25:18] Assocs to occurrences...
[INFO] [2019-10-11 23:25:18] Assocs to nodes...
[INFO] [2019-10-11 23:25:18] Assoc to sex term...
[INFO] [2019-10-11 23:25:18] Assoc to lifestage term...
[STOP] [2019-10-11 23:25:18] resolve_keys
[START] [2019-10-11 23:25:18] hold_for_later_1
[STOP] [2019-10-11 23:25:18] hold_for_later_1
[START] [2019-10-11 23:25:18] hold_for_later_2
[STOP] [2019-10-11 23:25:18] hold_for_later_2
[START] [2019-10-11 23:25:18] resolve_missing_parents
[STOP] [2019-10-11 23:25:28] resolve_missing_parents
[START] [2019-10-11 23:25:28] rebuild_nodes
[START] [2019-10-11 23:25:28] Flattener#flatten
[START] [2019-10-11 23:25:28] Flattener#study_resource
[START] [2019-10-11 23:25:28] Flattener#build_ancestry
[STOP] [2019-10-11 23:25:29] Flattener#build_ancestry
[INFO] [2019-10-11 23:25:29] 5184 ancestry keys
[START] [2019-10-11 23:25:29] build_node_ancestors
[INFO] [2019-10-11 23:25:29] old ancestors deleted.
[STOP] [2019-10-11 23:25:29] build_node_ancestors
[START] [2019-10-11 23:25:30] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 23:25:30] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 23:25:30] Flattener#flatten
[STOP] [2019-10-11 23:25:30] rebuild_nodes
[START] [2019-10-11 23:25:30] resolve_missing_media_owners
[STOP] [2019-10-11 23:25:30] resolve_missing_media_owners
[START] [2019-10-11 23:25:30] sanitize_media_verbatims
[STOP] [2019-10-11 23:25:30] sanitize_media_verbatims
[START] [2019-10-11 23:25:30] queue_downloads
[STOP] [2019-10-11 23:25:30] queue_downloads
[START] [2019-10-11 23:25:30] parse_names
[WARN] [2019-10-11 23:25:30] I see 5184 names which still need to be parsed.
[STOP] [2019-10-11 23:25:34] parse_names
[START] [2019-10-11 23:25:34] denormalize_canonical_names_to_nodes
[STOP] [2019-10-11 23:25:34] denormalize_canonical_names_to_nodes
[START] [2019-10-11 23:25:34] match_nodes
[START] [2019-10-11 23:25:34] map_all_nodes_to_pages
[STOP] [2019-10-11 23:28:24] map_all_nodes_to_pages
[INFO] [2019-10-11 23:28:24] 267 Unmatched nodes (of 5184)! That's too many to output. First 10: Gerbilliscus valida (#48984452); Myomys (#48984806); Bauhinia reticulatum (#48981638); Indigofera sericea (#48984195); Vigna adenanthum (#48986691); Vachellia raddiana (#48981789); Vachellia ehrenbergiana (#48984326); Acacia dudgeoni (#48981922); Acacia raddiana (#48982105); Acacia hockii (#48982119)
[START] [2019-10-11 23:28:24] update_nodes
[STOP] [2019-10-11 23:28:26] update_nodes
[STOP] [2019-10-11 23:28:26] match_nodes
[START] [2019-10-11 23:28:26] reindex_search
[STOP] [2019-10-11 23:28:34] reindex_search
[START] [2019-10-11 23:28:34] normalize_units
[STOP] [2019-10-11 23:28:34] normalize_units
[START] [2019-10-11 23:28:34] calculate_statistics
[STOP] [2019-10-11 23:28:34] calculate_statistics
[START] [2019-10-11 23:28:34] complete_harvest_instance
[START] [2019-10-11 23:28:34] overall_tsv_creation
[INFO] [2019-10-11 23:28:34] Processing group of 5184 in 1 batches of 10000
[INFO] [2019-10-11 23:29:43] 3374 Traits (unfiltered)...
[INFO] [2019-10-11 23:29:57] 3374 Traits (filtered)...
[INFO] [2019-10-11 23:29:57] 0 Associations (filtered)...
[INFO] [2019-10-11 23:30:41] 16867 metadata added.
[INFO] [2019-10-11 23:30:41] 0 metadata added.
[INFO] [2019-10-11 23:30:41] Average Time: 101.02
[INFO] [2019-10-11 23:30:41] Total Time: 2m7s
[STOP] [2019-10-11 23:30:41] overall_tsv_creation
[INFO] [2019-10-11 23:30:41] Done. Check your files:
[INFO] [2019-10-11 23:30:41] (5184 lines) /app/public/data/burkina_faso_sp_/publish_nodes.tsv
[INFO] [2019-10-11 23:30:41] (8186 lines) /app/public/data/burkina_faso_sp_/publish_node_ancestors.tsv
[INFO] [2019-10-11 23:30:41] (5184 lines) /app/public/data/burkina_faso_sp_/publish_scientific_names.tsv
[INFO] [2019-10-11 23:30:41] (3375 lines) /app/public/data/burkina_faso_sp_/publish_traits.tsv
[INFO] [2019-10-11 23:30:41] (16868 lines) /app/public/data/burkina_faso_sp_/publish_metadata.tsv
[STOP] [2019-10-11 23:30:41] complete_harvest_instance
[START] [2019-10-11 23:30:41] completed
[STOP] [2019-10-11 23:30:41] completed
[STOP] [2019-10-11 23:30:41] logged process, took 392.63

Latest Process