Harvest for Guinea Species List Created 13 Oct 06:49

Stage: completed
Fetched: 13 Oct 06:49
Validated: 13 Oct 06:49
Deltas Created 13 Oct 06:49
Units Normalized: 13 Oct 06:58
Ancestry Built: 13 Oct 06:51
Nodes Matched: 13 Oct 06:57
Names Parsed: 13 Oct 06:51
New Models Stored: 13 Oct 06:50
Indexed: 13 Oct 06:58
Completed: 13 Oct 07:00
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-13 06:49:39 -0400 by logger.rb/56815
[START] [2019-10-13 06:49:39] logged process
[START] [2019-10-13 06:49:39] create_harvest_instance
[STOP] [2019-10-13 06:49:40] create_harvest_instance
[START] [2019-10-13 06:49:40] fetch_files
[STOP] [2019-10-13 06:49:40] fetch_files
[START] [2019-10-13 06:49:40] validate_each_file
[STOP] [2019-10-13 06:49:41] validate_each_file
[START] [2019-10-13 06:49:41] convert_to_csv
[CMD] [2019-10-13 06:49:41] /usr/bin/sort /app/public/converted_csv/guinea_sp_list_refs_15939.csv > /app/public/converted_csv/guinea_sp_list_refs_15939.csv_sorted
[CMD] [2019-10-13 06:49:41] /usr/bin/sort /app/public/converted_csv/guinea_sp_list_nodes_15940.csv > /app/public/converted_csv/guinea_sp_list_nodes_15940.csv_sorted
[CMD] [2019-10-13 06:49:41] /usr/bin/sort /app/public/converted_csv/guinea_sp_list_occurrences_15941.csv > /app/public/converted_csv/guinea_sp_list_occurrences_15941.csv_sorted
[CMD] [2019-10-13 06:49:41] /usr/bin/sort /app/public/converted_csv/guinea_sp_list_measurements_15942.csv > /app/public/converted_csv/guinea_sp_list_measurements_15942.csv_sorted
[STOP] [2019-10-13 06:49:41] convert_to_csv
[START] [2019-10-13 06:49:41] calculate_delta
[CMD] [2019-10-13 06:49:41] echo "0a" > /app/public/diff/guinea_sp_list_refs_15939.diff
[CMD] [2019-10-13 06:49:41] tail -n +1 /app/public/converted_csv/guinea_sp_list_refs_15939.csv >> /app/public/diff/guinea_sp_list_refs_15939.diff
[CMD] [2019-10-13 06:49:41] echo "." >> /app/public/diff/guinea_sp_list_refs_15939.diff
[CMD] [2019-10-13 06:49:41] echo "0a" > /app/public/diff/guinea_sp_list_nodes_15940.diff
[CMD] [2019-10-13 06:49:41] tail -n +1 /app/public/converted_csv/guinea_sp_list_nodes_15940.csv >> /app/public/diff/guinea_sp_list_nodes_15940.diff
[CMD] [2019-10-13 06:49:41] echo "." >> /app/public/diff/guinea_sp_list_nodes_15940.diff
[CMD] [2019-10-13 06:49:42] echo "0a" > /app/public/diff/guinea_sp_list_occurrences_15941.diff
[CMD] [2019-10-13 06:49:42] tail -n +1 /app/public/converted_csv/guinea_sp_list_occurrences_15941.csv >> /app/public/diff/guinea_sp_list_occurrences_15941.diff
[CMD] [2019-10-13 06:49:42] echo "." >> /app/public/diff/guinea_sp_list_occurrences_15941.diff
[CMD] [2019-10-13 06:49:42] echo "0a" > /app/public/diff/guinea_sp_list_measurements_15942.diff
[CMD] [2019-10-13 06:49:42] tail -n +1 /app/public/converted_csv/guinea_sp_list_measurements_15942.csv >> /app/public/diff/guinea_sp_list_measurements_15942.diff
[CMD] [2019-10-13 06:49:42] echo "." >> /app/public/diff/guinea_sp_list_measurements_15942.diff
[STOP] [2019-10-13 06:49:42] calculate_delta
[START] [2019-10-13 06:49:42] parse_diff_and_store
[INFO] [2019-10-13 06:49:42] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 06:49:42] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 06:49:45] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 06:49:46] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 06:50:11] Storing 2 References
[INFO] [2019-10-13 06:50:11] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 06:50:11] Average Time: 0.0
[INFO] [2019-10-13 06:50:11] Total Time: 1s
[INFO] [2019-10-13 06:50:11] Storing 6644 ScientificNames
[INFO] [2019-10-13 06:50:11] Processing group of 6644 in 7 groups of 1000
[INFO] [2019-10-13 06:50:13] Average Time: 0.36
[INFO] [2019-10-13 06:50:13] Total Time: 3s
[INFO] [2019-10-13 06:50:13] last 3 / first 3: 0.77
[INFO] [2019-10-13 06:50:13] Std.Dev: 0.06324555320336758; Max: 0.44
[INFO] [2019-10-13 06:50:13] Storing 6644 Nodes
[INFO] [2019-10-13 06:50:13] Processing group of 6644 in 7 groups of 1000
[INFO] [2019-10-13 06:50:15] Average Time: 0.289
[INFO] [2019-10-13 06:50:15] Total Time: 3s
[INFO] [2019-10-13 06:50:15] last 3 / first 3: 0.91
[INFO] [2019-10-13 06:50:15] Std.Dev: 0.03162277660168379; Max: 0.32
[INFO] [2019-10-13 06:50:15] Storing 3856 Occurrences
[INFO] [2019-10-13 06:50:15] Processing group of 3856 in 4 groups of 1000
[INFO] [2019-10-13 06:50:16] Average Time: 0.105
[INFO] [2019-10-13 06:50:16] Total Time: 1s
[INFO] [2019-10-13 06:50:16] Storing 8412 TraitsReferences
[INFO] [2019-10-13 06:50:16] Processing group of 8412 in 9 groups of 1000
[INFO] [2019-10-13 06:50:16] Average Time: 0.074
[INFO] [2019-10-13 06:50:16] Total Time: 1s
[INFO] [2019-10-13 06:50:16] last 3 / first 3: 0.59
[INFO] [2019-10-13 06:50:16] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-13 06:50:16] Storing 8411 Traits
[INFO] [2019-10-13 06:50:16] Processing group of 8411 in 9 groups of 1000
[INFO] [2019-10-13 06:50:19] Average Time: 0.319
[INFO] [2019-10-13 06:50:19] Total Time: 3s
[INFO] [2019-10-13 06:50:19] last 3 / first 3: 0.67
[INFO] [2019-10-13 06:50:19] Std.Dev: 0.09486832980505137; Max: 0.5
[INFO] [2019-10-13 06:50:19] Storing 8408 MetaTraits
[INFO] [2019-10-13 06:50:19] Processing group of 8408 in 9 groups of 1000
[INFO] [2019-10-13 06:50:20] Average Time: 0.133
[INFO] [2019-10-13 06:50:20] Total Time: 2s
[INFO] [2019-10-13 06:50:20] last 3 / first 3: 0.7
[INFO] [2019-10-13 06:50:20] Std.Dev: 0.03162277660168379; Max: 0.17
[STOP] [2019-10-13 06:50:20] parse_diff_and_store
[START] [2019-10-13 06:50:20] resolve_keys
[INFO] [2019-10-13 06:50:51] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 06:50:54] traits to occurrences...
[INFO] [2019-10-13 06:50:55] traits to nodes (through occurrences)...
[INFO] [2019-10-13 06:50:55] Traits to sex term...
[INFO] [2019-10-13 06:50:57] Traits to lifestage term...
[INFO] [2019-10-13 06:50:58] MetaTraits to traits...
[INFO] [2019-10-13 06:50:59] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 06:51:00] Assocs to occurrences...
[INFO] [2019-10-13 06:51:00] Assocs to nodes...
[INFO] [2019-10-13 06:51:00] Assoc to sex term...
[INFO] [2019-10-13 06:51:00] Assoc to lifestage term...
[STOP] [2019-10-13 06:51:00] resolve_keys
[START] [2019-10-13 06:51:00] hold_for_later_1
[STOP] [2019-10-13 06:51:00] hold_for_later_1
[START] [2019-10-13 06:51:00] hold_for_later_2
[STOP] [2019-10-13 06:51:00] hold_for_later_2
[START] [2019-10-13 06:51:00] resolve_missing_parents
[STOP] [2019-10-13 06:51:16] resolve_missing_parents
[START] [2019-10-13 06:51:16] rebuild_nodes
[START] [2019-10-13 06:51:16] Flattener#flatten
[START] [2019-10-13 06:51:16] Flattener#study_resource
[START] [2019-10-13 06:51:16] Flattener#build_ancestry
[STOP] [2019-10-13 06:51:16] Flattener#build_ancestry
[INFO] [2019-10-13 06:51:16] 6644 ancestry keys
[START] [2019-10-13 06:51:16] build_node_ancestors
[INFO] [2019-10-13 06:51:16] old ancestors deleted.
[STOP] [2019-10-13 06:51:17] build_node_ancestors
[START] [2019-10-13 06:51:19] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 06:51:19] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 06:51:19] Flattener#flatten
[STOP] [2019-10-13 06:51:19] rebuild_nodes
[START] [2019-10-13 06:51:19] resolve_missing_media_owners
[STOP] [2019-10-13 06:51:19] resolve_missing_media_owners
[START] [2019-10-13 06:51:19] sanitize_media_verbatims
[STOP] [2019-10-13 06:51:19] sanitize_media_verbatims
[START] [2019-10-13 06:51:19] queue_downloads
[STOP] [2019-10-13 06:51:19] queue_downloads
[START] [2019-10-13 06:51:19] parse_names
[WARN] [2019-10-13 06:51:19] I see 6644 names which still need to be parsed.
[STOP] [2019-10-13 06:51:25] parse_names
[START] [2019-10-13 06:51:25] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 06:51:25] denormalize_canonical_names_to_nodes
[START] [2019-10-13 06:51:25] match_nodes
[START] [2019-10-13 06:51:25] map_all_nodes_to_pages
[STOP] [2019-10-13 06:57:57] map_all_nodes_to_pages
[INFO] [2019-10-13 06:57:57] 329 Unmatched nodes (of 6644)! That's too many to output. First 10: Bleda eximia (#49972642); Bleda canicapilla (#49973276); Bleda syndactyla (#49973296); Andropadus virens (#49969293); Andropadus latirostris (#49970417); Andropadus gracilirostris (#49970963); Andropadus gracilis (#49971356); Andropadus ansorgei (#49971758); Andropadus curvirostris (#49972657); Hirundo senegalensis (#49973407)
[START] [2019-10-13 06:57:57] update_nodes
[STOP] [2019-10-13 06:57:59] update_nodes
[STOP] [2019-10-13 06:57:59] match_nodes
[START] [2019-10-13 06:57:59] reindex_search
[STOP] [2019-10-13 06:58:17] reindex_search
[START] [2019-10-13 06:58:17] normalize_units
[STOP] [2019-10-13 06:58:17] normalize_units
[START] [2019-10-13 06:58:17] calculate_statistics
[STOP] [2019-10-13 06:58:17] calculate_statistics
[START] [2019-10-13 06:58:17] complete_harvest_instance
[START] [2019-10-13 06:58:17] overall_tsv_creation
[INFO] [2019-10-13 06:58:17] Processing group of 6644 in 1 batches of 10000
[INFO] [2019-10-13 06:59:31] 3856 Traits (unfiltered)...
[INFO] [2019-10-13 06:59:45] 3856 Traits (filtered)...
[INFO] [2019-10-13 06:59:45] 0 Associations (filtered)...
[INFO] [2019-10-13 07:00:31] 19276 metadata added.
[INFO] [2019-10-13 07:00:31] 0 metadata added.
[INFO] [2019-10-13 07:00:31] Average Time: 108.15
[INFO] [2019-10-13 07:00:31] Total Time: 2m14s
[STOP] [2019-10-13 07:00:31] overall_tsv_creation
[INFO] [2019-10-13 07:00:31] Done. Check your files:
[INFO] [2019-10-13 07:00:31] (6644 lines) /app/public/data/guinea_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 07:00:31] (16601 lines) /app/public/data/guinea_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 07:00:31] (6644 lines) /app/public/data/guinea_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 07:00:31] (3857 lines) /app/public/data/guinea_sp_list/publish_traits.tsv
[INFO] [2019-10-13 07:00:31] (19277 lines) /app/public/data/guinea_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 07:00:31] complete_harvest_instance
[START] [2019-10-13 07:00:31] completed
[STOP] [2019-10-13 07:00:31] completed
[STOP] [2019-10-13 07:00:31] logged process, took 652.25
Latest Process

13 Oct 06:49 EXITED currently processing 0