Stage:
completed
Fetched:
03 Apr 16:05
Validated:
03 Apr 16:05
Deltas Created
03 Apr 16:05
Units Normalized:
03 Apr 16:11
Ancestry Built:
03 Apr 16:08
Nodes Matched:
03 Apr 16:11
Names Parsed:
03 Apr 16:08
New Models Stored:
03 Apr 16:08
Indexed:
03 Apr 16:11
Completed:
03 Apr 16:22
Time to Harvest:
less than a minute
Harvesting Log
(608 lines)
# Logfile created on 2019-11-07 18:50:48 -0500 by logger.rb/56815
[START] [2019-11-07 18:50:48] logged process
[START] [2019-11-07 18:50:48] create_harvest_instance
[STOP] [2019-11-07 18:50:52] create_harvest_instance
[START] [2019-11-07 18:50:52] fetch_files
[STOP] [2019-11-07 18:50:52] fetch_files
[START] [2019-11-07 18:50:52] validate_each_file
[STOP] [2019-11-07 18:51:06] validate_each_file
[START] [2019-11-07 18:51:06] convert_to_csv
[CMD] [2019-11-07 18:51:06] /usr/bin/sort /app/public/converted_csv/NMNHGrowthForm_agents_18430.csv > /app/public/converted_csv/NMNHGrowthForm_agents_18430.csv_sorted
[CMD] [2019-11-07 18:51:06] /usr/bin/sort /app/public/converted_csv/NMNHGrowthForm_refs_18431.csv > /app/public/converted_csv/NMNHGrowthForm_refs_18431.csv_sorted
[CMD] [2019-11-07 18:51:06] /usr/bin/sort /app/public/converted_csv/NMNHGrowthForm_nodes_18432.csv > /app/public/converted_csv/NMNHGrowthForm_nodes_18432.csv_sorted
[CMD] [2019-11-07 18:51:06] /usr/bin/sort /app/public/converted_csv/NMNHGrowthForm_media_18433.csv > /app/public/converted_csv/NMNHGrowthForm_media_18433.csv_sorted
[CMD] [2019-11-07 18:51:06] /usr/bin/sort /app/public/converted_csv/NMNHGrowthForm_vernaculars_18434.csv > /app/public/converted_csv/NMNHGrowthForm_vernaculars_18434.csv_sorted
[CMD] [2019-11-07 18:51:06] /usr/bin/sort /app/public/converted_csv/NMNHGrowthForm_occurrences_18435.csv > /app/public/converted_csv/NMNHGrowthForm_occurrences_18435.csv_sorted
[CMD] [2019-11-07 18:51:06] /usr/bin/sort /app/public/converted_csv/NMNHGrowthForm_assocs_18436.csv > /app/public/converted_csv/NMNHGrowthForm_assocs_18436.csv_sorted
[CMD] [2019-11-07 18:51:06] /usr/bin/sort /app/public/converted_csv/NMNHGrowthForm_measurements_18437.csv > /app/public/converted_csv/NMNHGrowthForm_measurements_18437.csv_sorted
[STOP] [2019-11-07 18:51:06] convert_to_csv
[START] [2019-11-07 18:51:06] calculate_delta
[CMD] [2019-11-07 18:51:06] echo "0a" > /app/public/diff/NMNHGrowthForm_agents_18430.diff
[CMD] [2019-11-07 18:51:06] tail -n +1 /app/public/converted_csv/NMNHGrowthForm_agents_18430.csv >> /app/public/diff/NMNHGrowthForm_agents_18430.diff
[CMD] [2019-11-07 18:51:06] echo "." >> /app/public/diff/NMNHGrowthForm_agents_18430.diff
[CMD] [2019-11-07 18:51:06] echo "0a" > /app/public/diff/NMNHGrowthForm_refs_18431.diff
[CMD] [2019-11-07 18:51:06] tail -n +1 /app/public/converted_csv/NMNHGrowthForm_refs_18431.csv >> /app/public/diff/NMNHGrowthForm_refs_18431.diff
[CMD] [2019-11-07 18:51:06] echo "." >> /app/public/diff/NMNHGrowthForm_refs_18431.diff
[CMD] [2019-11-07 18:51:06] echo "0a" > /app/public/diff/NMNHGrowthForm_nodes_18432.diff
[CMD] [2019-11-07 18:51:06] tail -n +1 /app/public/converted_csv/NMNHGrowthForm_nodes_18432.csv >> /app/public/diff/NMNHGrowthForm_nodes_18432.diff
[CMD] [2019-11-07 18:51:06] echo "." >> /app/public/diff/NMNHGrowthForm_nodes_18432.diff
[CMD] [2019-11-07 18:51:06] echo "0a" > /app/public/diff/NMNHGrowthForm_media_18433.diff
[CMD] [2019-11-07 18:51:06] tail -n +1 /app/public/converted_csv/NMNHGrowthForm_media_18433.csv >> /app/public/diff/NMNHGrowthForm_media_18433.diff
[CMD] [2019-11-07 18:51:06] echo "." >> /app/public/diff/NMNHGrowthForm_media_18433.diff
[CMD] [2019-11-07 18:51:06] echo "0a" > /app/public/diff/NMNHGrowthForm_vernaculars_18434.diff
[CMD] [2019-11-07 18:51:06] tail -n +1 /app/public/converted_csv/NMNHGrowthForm_vernaculars_18434.csv >> /app/public/diff/NMNHGrowthForm_vernaculars_18434.diff
[CMD] [2019-11-07 18:51:06] echo "." >> /app/public/diff/NMNHGrowthForm_vernaculars_18434.diff
[CMD] [2019-11-07 18:51:06] echo "0a" > /app/public/diff/NMNHGrowthForm_occurrences_18435.diff
[CMD] [2019-11-07 18:51:06] tail -n +1 /app/public/converted_csv/NMNHGrowthForm_occurrences_18435.csv >> /app/public/diff/NMNHGrowthForm_occurrences_18435.diff
[CMD] [2019-11-07 18:51:06] echo "." >> /app/public/diff/NMNHGrowthForm_occurrences_18435.diff
[CMD] [2019-11-07 18:51:06] echo "0a" > /app/public/diff/NMNHGrowthForm_assocs_18436.diff
[CMD] [2019-11-07 18:51:06] tail -n +1 /app/public/converted_csv/NMNHGrowthForm_assocs_18436.csv >> /app/public/diff/NMNHGrowthForm_assocs_18436.diff
[CMD] [2019-11-07 18:51:06] echo "." >> /app/public/diff/NMNHGrowthForm_assocs_18436.diff
[CMD] [2019-11-07 18:51:06] echo "0a" > /app/public/diff/NMNHGrowthForm_measurements_18437.diff
[CMD] [2019-11-07 18:51:06] tail -n +1 /app/public/converted_csv/NMNHGrowthForm_measurements_18437.csv >> /app/public/diff/NMNHGrowthForm_measurements_18437.diff
[CMD] [2019-11-07 18:51:06] echo "." >> /app/public/diff/NMNHGrowthForm_measurements_18437.diff
[STOP] [2019-11-07 18:51:06] calculate_delta
[START] [2019-11-07 18:51:06] parse_diff_and_store
[INFO] [2019-11-07 18:51:06] Loading agents diff file into memory (true lines)...
[INFO] [2019-11-07 18:51:06] Loading refs diff file into memory (true lines)...
[INFO] [2019-11-07 18:51:06] Loading nodes diff file into memory (true lines)...
[WARN] [2019-11-07 18:51:07] Filtered Scientific Name `Astilbe rubra Hook. f. & ex Hook.` to `Astilbe rubra Hook. f. & ex Hook.`
[WARN] [2019-11-07 18:51:11] Filtered Scientific Name `Schwenckia elegans Carvalho` to `Schwenckia elegans Carvalho`
[WARN] [2019-11-07 18:51:11] Filtered Scientific Name `Solanum davidsei Carvalho` to `Solanum davidsei Carvalho`
[INFO] [2019-11-07 18:51:12] Loading media diff file into memory (true lines)...
[INFO] [2019-11-07 18:51:12] Loading vernaculars diff file into memory (true lines)...
[INFO] [2019-11-07 18:51:12] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-11-07 18:51:23] Loading assocs diff file into memory (true lines)...
[INFO] [2019-11-07 18:51:23] Loading measurements diff file into memory (true lines)...
[INFO] [2019-11-07 18:56:25] Storing 15532 ScientificNames
[INFO] [2019-11-07 18:56:25] Processing group of 15532 in 16 groups of 1000
[INFO] [2019-11-07 18:56:31] Average Time: 0.363
[INFO] [2019-11-07 18:56:31] Total Time: 6s
[INFO] [2019-11-07 18:56:31] last 3 / first 3: 0.86
[INFO] [2019-11-07 18:56:31] Std.Dev: 0.06324555320336758; Max: 0.47
[INFO] [2019-11-07 18:56:31] Storing 15532 Nodes
[INFO] [2019-11-07 18:56:31] Processing group of 15532 in 16 groups of 1000
[INFO] [2019-11-07 18:56:36] Average Time: 0.291
[INFO] [2019-11-07 18:56:36] Total Time: 5s
[INFO] [2019-11-07 18:56:36] last 3 / first 3: 0.82
[INFO] [2019-11-07 18:56:36] Std.Dev: 0.044721359549995794; Max: 0.34
[INFO] [2019-11-07 18:56:36] Storing 55999 Occurrences
[INFO] [2019-11-07 18:56:36] Processing group of 55999 in 56 groups of 1000
[INFO] [2019-11-07 18:56:44] Average Time: 0.147
[INFO] [2019-11-07 18:56:44] Total Time: 9s
[INFO] [2019-11-07 18:56:44] last 3 / first 3: 0.88
[INFO] [2019-11-07 18:56:44] Std.Dev: 0.11401754250991379; Max: 0.96
[INFO] [2019-11-07 18:56:44] Storing 55999 Traits
[INFO] [2019-11-07 18:56:44] Processing group of 55999 in 56 groups of 1000
[INFO] [2019-11-07 18:57:03] Average Time: 0.338
[INFO] [2019-11-07 18:57:03] Total Time: 20s
[INFO] [2019-11-07 18:57:03] last 3 / first 3: 0.89
[INFO] [2019-11-07 18:57:03] Std.Dev: 0.08944271909999159; Max: 0.67
[INFO] [2019-11-07 18:57:03] Storing 167997 MetaTraits
[INFO] [2019-11-07 18:57:03] Processing group of 167997 in 168 groups of 1000
[INFO] [2019-11-07 18:57:24] Average Time: 0.119
[INFO] [2019-11-07 18:57:24] Total Time: 21s
[INFO] [2019-11-07 18:57:24] last 3 / first 3: 0.79
[INFO] [2019-11-07 18:57:24] Std.Dev: 0.09486832980505137; Max: 1.31
[STOP] [2019-11-07 18:57:24] parse_diff_and_store
[START] [2019-11-07 18:57:24] resolve_keys
[INFO] [2019-11-07 18:57:32] Occurrences to nodes (through scientific_names)...
[INFO] [2019-11-07 18:57:33] traits to occurrences...
[INFO] [2019-11-07 18:57:37] traits to nodes (through occurrences)...
[INFO] [2019-11-07 18:57:39] Traits to sex term...
[INFO] [2019-11-07 18:57:40] Traits to lifestage term...
[INFO] [2019-11-07 18:57:40] MetaTraits to traits...
[INFO] [2019-11-07 18:57:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-11-07 18:57:51] Assocs to occurrences...
[INFO] [2019-11-07 18:57:51] Assocs to nodes...
[INFO] [2019-11-07 18:57:51] Assoc to sex term...
[INFO] [2019-11-07 18:57:51] Assoc to lifestage term...
[STOP] [2019-11-07 18:57:51] resolve_keys
[START] [2019-11-07 18:57:51] hold_for_later_1
[STOP] [2019-11-07 18:57:51] hold_for_later_1
[START] [2019-11-07 18:57:51] hold_for_later_2
[STOP] [2019-11-07 18:57:51] hold_for_later_2
[START] [2019-11-07 18:57:51] resolve_missing_parents
[STOP] [2019-11-07 18:57:51] resolve_missing_parents
[START] [2019-11-07 18:57:51] rebuild_nodes
[START] [2019-11-07 18:57:51] Flattener#flatten
[START] [2019-11-07 18:57:51] Flattener#study_resource
[START] [2019-11-07 18:57:52] Flattener#build_ancestry
[STOP] [2019-11-07 18:57:54] Flattener#build_ancestry
[INFO] [2019-11-07 18:57:54] 15532 ancestry keys
[START] [2019-11-07 18:57:54] build_node_ancestors
[INFO] [2019-11-07 18:57:54] old ancestors deleted.
[STOP] [2019-11-07 18:57:55] build_node_ancestors
[START] [2019-11-07 18:57:56] Flattener#propagate_ancestor_ids
[STOP] [2019-11-07 18:57:56] Flattener#propagate_ancestor_ids
[STOP] [2019-11-07 18:57:56] Flattener#flatten
[STOP] [2019-11-07 18:57:56] rebuild_nodes
[START] [2019-11-07 18:57:56] resolve_missing_media_owners
[STOP] [2019-11-07 18:57:56] resolve_missing_media_owners
[START] [2019-11-07 18:57:56] sanitize_media_verbatims
[STOP] [2019-11-07 18:57:56] sanitize_media_verbatims
[START] [2019-11-07 18:57:56] queue_downloads
[STOP] [2019-11-07 18:57:56] queue_downloads
[START] [2019-11-07 18:57:56] parse_names
[WARN] [2019-11-07 18:57:56] I see 15532 names which still need to be parsed.
[STOP] [2019-11-07 18:58:09] parse_names
[START] [2019-11-07 18:58:09] denormalize_canonical_names_to_nodes
[STOP] [2019-11-07 18:58:09] denormalize_canonical_names_to_nodes
[START] [2019-11-07 18:58:09] match_nodes
[START] [2019-11-07 18:58:09] map_all_nodes_to_pages
[STOP] [2019-11-07 19:13:44] map_all_nodes_to_pages
[INFO] [2019-11-07 19:13:44] 1065 Unmatched nodes (of 15532)! That's too many to output. First 10: Abarema aspleniifolia (#54749446); Abarema mataybifolia (#54749451); Abildgaardia (#54749470); Abroma (#54749474); Acacia angulosa (#54749498); Acacia angustissima angustissima (#54749500); Acacia angustissima smithii (#54749502); Acacia angustissima angustissima (#54749503); Acacia cuernavacana (#54749525); Acacia elegans (#54749529)
[START] [2019-11-07 19:13:44] update_nodes
[STOP] [2019-11-07 19:13:49] update_nodes
[STOP] [2019-11-07 19:13:49] match_nodes
[START] [2019-11-07 19:13:49] reindex_search
[STOP] [2019-11-07 19:14:14] reindex_search
[START] [2019-11-07 19:14:14] normalize_units
[STOP] [2019-11-07 19:14:14] normalize_units
[START] [2019-11-07 19:14:14] calculate_statistics
[STOP] [2019-11-07 19:14:14] calculate_statistics
[START] [2019-11-07 19:14:14] complete_harvest_instance
[START] [2019-11-07 19:14:14] overall_tsv_creation
[INFO] [2019-11-07 19:14:15] Processing group of 15532 in 2 batches of 10000
[INFO] [2019-11-07 19:15:42] 34956 Traits (unfiltered)...
[INFO] [2019-11-07 19:15:55] 34956 Traits (filtered)...
[INFO] [2019-11-07 19:15:55] 0 Associations (filtered)...
[INFO] [2019-11-07 19:17:32] 104868 metadata added.
[INFO] [2019-11-07 19:17:32] 0 metadata added.
[INFO] [2019-11-07 19:18:41] 21043 Traits (unfiltered)...
[INFO] [2019-11-07 19:18:54] 21043 Traits (filtered)...
[INFO] [2019-11-07 19:18:54] 0 Associations (filtered)...
[INFO] [2019-11-07 19:20:08] 63129 metadata added.
[INFO] [2019-11-07 19:20:08] 0 metadata added.
[INFO] [2019-11-07 19:20:08] Average Time: 150.835
[INFO] [2019-11-07 19:20:08] Total Time: 5m54s
[STOP] [2019-11-07 19:20:08] overall_tsv_creation
[INFO] [2019-11-07 19:20:08] Done. Check your files:
[INFO] [2019-11-07 19:20:08] (15532 lines) /app/public/data/NMNHGrowthForm/publish_nodes.tsv
[INFO] [2019-11-07 19:20:08] (12698 lines) /app/public/data/NMNHGrowthForm/publish_node_ancestors.tsv
[INFO] [2019-11-07 19:20:09] (15532 lines) /app/public/data/NMNHGrowthForm/publish_scientific_names.tsv
[INFO] [2019-11-07 19:20:09] (56000 lines) /app/public/data/NMNHGrowthForm/publish_traits.tsv
[INFO] [2019-11-07 19:20:09] (167998 lines) /app/public/data/NMNHGrowthForm/publish_metadata.tsv
[STOP] [2019-11-07 19:20:09] complete_harvest_instance
[START] [2019-11-07 19:20:09] completed
[STOP] [2019-11-07 19:20:09] completed
[STOP] [2019-11-07 19:20:09] logged process, took 1760.82
[INFO] [2021-01-28 11:33:47] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-01-28 11:33:47] ## remove_type: ScientificName
[INFO] [2021-01-28 11:33:47] ++ Calling delete_all on 15532 instances...
[INFO] [2021-01-28 11:33:49] [11:33:49.088] Removed 15532 Scientificnames
[INFO] [2021-01-28 11:33:49] ## remove_type: Vernacular
[INFO] [2021-01-28 11:33:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-01-28 11:33:49] [11:33:49.092] Removed 0 Vernaculars
[INFO] [2021-01-28 11:33:49] ## remove_type: Article
[INFO] [2021-01-28 11:33:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-01-28 11:33:49] [11:33:49.095] Removed 0 Articles
[INFO] [2021-01-28 11:33:49] ## remove_type: Medium
[INFO] [2021-01-28 11:33:49] ++ Calling delete_all on 0 instances...
[INFO] [2021-01-28 11:33:49] [11:33:49.099] Removed 0 Media
[INFO] [2021-01-28 11:33:49] ## remove_type: Trait
[INFO] [2021-01-28 11:33:49] ++ Calling delete_all on 55999 instances...
[INFO] [2021-01-28 11:33:58] [11:33:58.785] Removed 55999 Traits
[INFO] [2021-01-28 11:33:58] ## remove_type: MetaTrait
[INFO] [2021-01-28 11:33:58] ++ Calling delete_all on 167997 instances...
[INFO] [2021-01-28 11:34:10] [11:34:10.072] Removed 167997 Metatraits
[INFO] [2021-01-28 11:34:10] ## remove_type: OccurrenceMetadatum
[INFO] [2021-01-28 11:34:10] ++ Calling delete_all on 0 instances...
[INFO] [2021-01-28 11:34:10] [11:34:10.167] Removed 0 Occurrencemetadata
[INFO] [2021-01-28 11:34:10] ## remove_type: Assoc
[INFO] [2021-01-28 11:34:10] ++ Calling delete_all on 0 instances...
[INFO] [2021-01-28 11:34:10] [11:34:10.170] Removed 0 Assocs
[INFO] [2021-01-28 11:34:10] ## remove_type: MetaAssoc
[INFO] [2021-01-28 11:34:10] ++ Calling delete_all on 0 instances...
[INFO] [2021-01-28 11:34:10] [11:34:10.172] Removed 0 Metaassocs
[INFO] [2021-01-28 11:34:10] ## remove_type: Identifier
[INFO] [2021-01-28 11:34:10] ++ Calling delete_all on 0 instances...
[INFO] [2021-01-28 11:34:10] [11:34:10.188] Removed 0 Identifiers
[INFO] [2021-01-28 11:34:10] ## remove_type: Reference
[INFO] [2021-01-28 11:34:10] ++ Calling delete_all on 0 instances...
[INFO] [2021-01-28 11:34:10] [11:34:10.191] Removed 0 References
[INFO] [2021-01-28 11:34:10] Starting batch with ID 54753445...
[INFO] [2021-01-28 11:34:11] Starting batch with ID 54753180...
[INFO] [2021-01-28 11:34:13] Starting batch with ID 54755683...
[INFO] [2021-01-28 11:34:14] Starting batch with ID 54762665...
[INFO] [2021-01-28 11:34:14] Starting batch with ID 54762665...
[INFO] [2021-01-28 11:34:15] ## remove_type: Node
[INFO] [2021-01-28 11:34:15] ++ Calling delete_all on 15532 instances...
[INFO] [2021-01-28 11:34:16] [11:34:16.384] Removed 15532 Nodes
[START] [2021-01-28 11:34:20] logged process: e38687fde360d9ce2f48dd55c3bf56ebb9d8efa6
[START] [2021-01-28 11:34:20] Creating resource from OpenData
[START] [2021-01-28 11:34:21] logged process: e38687fde360d9ce2f48dd55c3bf56ebb9d8efa6
[START] [2021-01-28 11:34:21] Parse meta.xml file and create formats with fields
[WARN] [2021-01-28 11:34:21] (common) IGNORED (occurrences) field header: eventID term: http://rs.tdwg.org/dwc/terms/eventID
[STOP] [2021-01-28 11:34:21] Parse meta.xml file and create formats with fields
[STOP] [2021-01-28 11:34:21] Creating resource from OpenData
[START] [2021-01-28 11:34:21] logged process: e38687fde360d9ce2f48dd55c3bf56ebb9d8efa6
[START] [2021-01-28 11:34:21] create_harvest_instance
[STOP] [2021-01-28 11:34:26] create_harvest_instance
[START] [2021-01-28 11:34:26] fetch_files
[STOP] [2021-01-28 11:34:26] fetch_files
[START] [2021-01-28 11:34:26] validate_each_file
[STOP] [2021-01-28 11:34:44] validate_each_file
[START] [2021-01-28 11:34:44] convert_to_csv
[CMD] [2021-01-28 11:34:44] /usr/bin/sort /app/public/converted_csv/NMNHGrowthForm_nodes_26281.csv > /app/public/converted_csv/NMNHGrowthForm_nodes_26281.csv_sorted
[CMD] [2021-01-28 11:34:44] /usr/bin/sort /app/public/converted_csv/NMNHGrowthForm_occurrences_26282.csv > /app/public/converted_csv/NMNHGrowthForm_occurrences_26282.csv_sorted
[CMD] [2021-01-28 11:34:44] /usr/bin/sort /app/public/converted_csv/NMNHGrowthForm_measurements_26283.csv > /app/public/converted_csv/NMNHGrowthForm_measurements_26283.csv_sorted
[STOP] [2021-01-28 11:34:45] convert_to_csv
[START] [2021-01-28 11:34:45] calculate_delta
[CMD] [2021-01-28 11:34:45] echo "0a" > /app/public/diff/NMNHGrowthForm_nodes_26281.diff
[CMD] [2021-01-28 11:34:45] tail -n +1 /app/public/converted_csv/NMNHGrowthForm_nodes_26281.csv >> /app/public/diff/NMNHGrowthForm_nodes_26281.diff
[CMD] [2021-01-28 11:34:45] echo "." >> /app/public/diff/NMNHGrowthForm_nodes_26281.diff
[CMD] [2021-01-28 11:34:45] echo "0a" > /app/public/diff/NMNHGrowthForm_occurrences_26282.diff
[CMD] [2021-01-28 11:34:45] tail -n +1 /app/public/converted_csv/NMNHGrowthForm_occurrences_26282.csv >> /app/public/diff/NMNHGrowthForm_occurrences_26282.diff
[CMD] [2021-01-28 11:34:45] echo "." >> /app/public/diff/NMNHGrowthForm_occurrences_26282.diff
[CMD] [2021-01-28 11:34:45] echo "0a" > /app/public/diff/NMNHGrowthForm_measurements_26283.diff
[CMD] [2021-01-28 11:34:45] tail -n +1 /app/public/converted_csv/NMNHGrowthForm_measurements_26283.csv >> /app/public/diff/NMNHGrowthForm_measurements_26283.diff
[CMD] [2021-01-28 11:34:45] echo "." >> /app/public/diff/NMNHGrowthForm_measurements_26283.diff
[STOP] [2021-01-28 11:34:45] calculate_delta
[START] [2021-01-28 11:34:45] parse_diff_and_store
[INFO] [2021-01-28 11:34:45] Loading nodes diff file into memory (true lines)...
[WARN] [2021-01-28 11:34:45] Filtered Scientific Name `Astilbe rubra Hook. f. & ex Hook.` to `Astilbe rubra Hook. f. & ex Hook.`
[WARN] [2021-01-28 11:34:48] Filtered Scientific Name `Schwenckia elegans Carvalho` to `Schwenckia elegans Carvalho`
[WARN] [2021-01-28 11:34:49] Filtered Scientific Name `Solanum davidsei Carvalho` to `Solanum davidsei Carvalho`
[INFO] [2021-01-28 11:34:49] Loading occurrences diff file into memory (true lines)...
[INFO] [2021-01-28 11:34:57] Loading measurements diff file into memory (true lines)...
[INFO] [2021-01-28 11:35:50] Storing 15532 ScientificNames
[INFO] [2021-01-28 11:35:50] Processing group of 15532 in 16 groups of 1000
[INFO] [2021-01-28 11:35:55] Average Time: 0.299
[INFO] [2021-01-28 11:35:55] Total Time: 5s
[INFO] [2021-01-28 11:35:55] last 3 / first 3: 0.87
[INFO] [2021-01-28 11:35:55] Std.Dev: 0.044721359549995794; Max: 0.39
[INFO] [2021-01-28 11:35:55] Storing 15532 Nodes
[INFO] [2021-01-28 11:35:55] Processing group of 15532 in 16 groups of 1000
[INFO] [2021-01-28 11:36:03] Average Time: 0.519
[INFO] [2021-01-28 11:36:03] Total Time: 9s
[INFO] [2021-01-28 11:36:03] last 3 / first 3: 0.55
[INFO] [2021-01-28 11:36:03] Std.Dev: 0.5422176684690383; Max: 2.33
[INFO] [2021-01-28 11:36:03] Storing 55999 Occurrences
[INFO] [2021-01-28 11:36:03] Processing group of 55999 in 56 groups of 1000
[INFO] [2021-01-28 11:36:10] Average Time: 0.112
[INFO] [2021-01-28 11:36:10] Total Time: 7s
[INFO] [2021-01-28 11:36:10] last 3 / first 3: 1.0
[INFO] [2021-01-28 11:36:10] Std.Dev: 0.0; Max: 0.2
[INFO] [2021-01-28 11:36:10] Storing 108605 OccurrenceMetadata
[INFO] [2021-01-28 11:36:10] Processing group of 108605 in 109 groups of 1000
[INFO] [2021-01-28 11:36:24] Average Time: 0.131
[INFO] [2021-01-28 11:36:24] Total Time: 15s
[INFO] [2021-01-28 11:36:24] last 3 / first 3: 0.89
[INFO] [2021-01-28 11:36:24] Std.Dev: 0.044721359549995794; Max: 0.38
[INFO] [2021-01-28 11:36:24] Storing 55999 Traits
[INFO] [2021-01-28 11:36:24] Processing group of 55999 in 56 groups of 1000
[INFO] [2021-01-28 11:36:43] Average Time: 0.324
[INFO] [2021-01-28 11:36:43] Total Time: 19s
[INFO] [2021-01-28 11:36:43] last 3 / first 3: 1.1
[INFO] [2021-01-28 11:36:43] Std.Dev: 0.18708286933869708; Max: 1.64
[INFO] [2021-01-28 11:36:43] Storing 111998 MetaTraits
[INFO] [2021-01-28 11:36:43] Processing group of 111998 in 112 groups of 1000
[INFO] [2021-01-28 11:36:56] Average Time: 0.116
[INFO] [2021-01-28 11:36:56] Total Time: 14s
[INFO] [2021-01-28 11:36:56] last 3 / first 3: 1.0
[INFO] [2021-01-28 11:36:56] Std.Dev: 0.0; Max: 0.22
[STOP] [2021-01-28 11:36:56] parse_diff_and_store
[START] [2021-01-28 11:36:56] resolve_keys
[INFO] [2021-01-28 11:37:05] Occurrences to nodes (through scientific_names)...
[INFO] [2021-01-28 11:37:10] traits to occurrences...
[INFO] [2021-01-28 11:37:12] traits to nodes (through occurrences)...
[INFO] [2021-01-28 11:37:13] Traits to sex term...
[INFO] [2021-01-28 11:37:14] Traits to lifestage term...
[INFO] [2021-01-28 11:37:14] MetaTraits to traits...
[INFO] [2021-01-28 11:37:17] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-01-28 11:37:17] Assocs to occurrences...
[INFO] [2021-01-28 11:37:17] Assocs to nodes...
[INFO] [2021-01-28 11:37:17] Assoc to sex term...
[INFO] [2021-01-28 11:37:17] Assoc to lifestage term...
[INFO] [2021-01-28 11:37:17] MetaAssoc to assocs...
[STOP] [2021-01-28 11:37:17] resolve_keys
[START] [2021-01-28 11:37:17] hold_for_later_1
[STOP] [2021-01-28 11:37:17] hold_for_later_1
[START] [2021-01-28 11:37:17] hold_for_later_2
[STOP] [2021-01-28 11:37:17] hold_for_later_2
[START] [2021-01-28 11:37:17] resolve_missing_parents
[STOP] [2021-01-28 11:37:17] resolve_missing_parents
[START] [2021-01-28 11:37:17] rebuild_nodes
[START] [2021-01-28 11:37:17] Flattener#flatten
[START] [2021-01-28 11:37:17] Flattener#study_resource
[START] [2021-01-28 11:37:17] Flattener#build_ancestry
[STOP] [2021-01-28 11:37:21] Flattener#build_ancestry
[INFO] [2021-01-28 11:37:21] 15532 ancestry keys
[START] [2021-01-28 11:37:21] build_node_ancestors
[INFO] [2021-01-28 11:37:21] old ancestors deleted.
[STOP] [2021-01-28 11:37:21] build_node_ancestors
[START] [2021-01-28 11:37:22] Flattener#propagate_ancestor_ids
[STOP] [2021-01-28 11:37:22] Flattener#propagate_ancestor_ids
[STOP] [2021-01-28 11:37:22] Flattener#flatten
[STOP] [2021-01-28 11:37:22] rebuild_nodes
[START] [2021-01-28 11:37:22] resolve_missing_media_owners
[STOP] [2021-01-28 11:37:22] resolve_missing_media_owners
[START] [2021-01-28 11:37:22] sanitize_media_verbatims
[STOP] [2021-01-28 11:37:22] sanitize_media_verbatims
[START] [2021-01-28 11:37:22] queue_downloads
[STOP] [2021-01-28 11:37:22] queue_downloads
[START] [2021-01-28 11:37:22] parse_names
[WARN] [2021-01-28 11:37:22] I see 15532 names which still need to be parsed.
[STOP] [2021-01-28 11:37:37] parse_names
[START] [2021-01-28 11:37:37] denormalize_canonical_names_to_nodes
[STOP] [2021-01-28 11:37:38] denormalize_canonical_names_to_nodes
[START] [2021-01-28 11:37:38] match_nodes
[START] [2021-01-28 11:37:38] map_all_nodes_to_pages
[STOP] [2021-01-28 12:13:16] map_all_nodes_to_pages
[INFO] [2021-01-28 12:13:16] 1372 Unmatched nodes (of 15532)! That's too many to output. Full list in /app/public/data/NMNHGrowthForm/unmatched_nodes.txt ; First 10: Abarema aspleniifolia (#87656639); Abarema mataybifolia (#87656644); Abelmoschus moschatus (#87656653); Abies ernestii salouensis (#87656655); Abildgaardia (#87656663); Abroma (#87656667); Abroma augustum (#87656668); Abutilon sandwicense (#87656686); Acacia angulosa (#87656691); Acacia angustissima angustissima (#87656693)
[START] [2021-01-28 12:13:16] update_nodes
[STOP] [2021-01-28 12:13:22] update_nodes
[STOP] [2021-01-28 12:13:22] match_nodes
[START] [2021-01-28 12:13:22] reindex_search
[STOP] [2021-01-28 12:14:02] reindex_search
[START] [2021-01-28 12:14:02] normalize_units
[STOP] [2021-01-28 12:14:02] normalize_units
[START] [2021-01-28 12:14:02] calculate_statistics
[STOP] [2021-01-28 12:14:02] calculate_statistics
[START] [2021-01-28 12:14:02] complete_harvest_instance
[START] [2021-01-28 12:14:02] overall_tsv_creation
[INFO] [2021-01-28 12:14:02] Processing group of 15532 in 2 batches of 10000
[INFO] [2021-01-28 12:15:11] 34956 Traits (unfiltered)...
[INFO] [2021-01-28 12:18:08] 34956 Traits (filtered)...
[INFO] [2021-01-28 12:18:08] 0 Associations (filtered)...
[INFO] [2021-01-28 12:18:23] 137927 metadata added.
[INFO] [2021-01-28 12:18:23] 0 metadata added.
[INFO] [2021-01-28 12:19:59] 21043 Traits (unfiltered)...
[INFO] [2021-01-28 12:22:03] 21043 Traits (filtered)...
[INFO] [2021-01-28 12:22:03] 0 Associations (filtered)...
[INFO] [2021-01-28 12:22:12] 82676 metadata added.
[INFO] [2021-01-28 12:22:12] 0 metadata added.
[INFO] [2021-01-28 12:22:49] Average Time: 233.145
[INFO] [2021-01-28 12:22:49] Total Time: 8m47s
[STOP] [2021-01-28 12:22:49] overall_tsv_creation
[INFO] [2021-01-28 12:22:49] Done. Check your files:
[INFO] [2021-01-28 12:22:49] (15532 lines) /app/public/data/NMNHGrowthForm/publish_nodes.tsv
[INFO] [2021-01-28 12:22:49] (12698 lines) /app/public/data/NMNHGrowthForm/publish_node_ancestors.tsv
[INFO] [2021-01-28 12:22:49] (15532 lines) /app/public/data/NMNHGrowthForm/publish_scientific_names.tsv
[INFO] [2021-01-28 12:22:49] (56000 lines) /app/public/data/NMNHGrowthForm/publish_traits.tsv
[INFO] [2021-01-28 12:22:49] (220604 lines) /app/public/data/NMNHGrowthForm/publish_metadata.tsv
[STOP] [2021-01-28 12:22:50] complete_harvest_instance
[START] [2021-01-28 12:22:50] completed
[STOP] [2021-01-28 12:22:50] completed
[STOP] [2021-01-28 12:22:50] logged process, took 2908.36
[INFO] [2021-04-03 16:04:42] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-03 16:04:43] ## remove_type: ScientificName
[INFO] [2021-04-03 16:04:43] ++ Calling delete_all on 15532 instances...
[INFO] [2021-04-03 16:04:45] [16:04:45.512] Removed 15532 Scientificnames
[INFO] [2021-04-03 16:04:45] ## remove_type: Vernacular
[INFO] [2021-04-03 16:04:45] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-03 16:04:45] [16:04:45.513] Removed 0 Vernaculars
[INFO] [2021-04-03 16:04:45] ## remove_type: Article
[INFO] [2021-04-03 16:04:45] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-03 16:04:45] [16:04:45.515] Removed 0 Articles
[INFO] [2021-04-03 16:04:45] ## remove_type: Medium
[INFO] [2021-04-03 16:04:45] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-03 16:04:45] [16:04:45.516] Removed 0 Media
[INFO] [2021-04-03 16:04:45] ## remove_type: Trait
[INFO] [2021-04-03 16:04:45] ++ Calling delete_all on 55999 instances...
[INFO] [2021-04-03 16:05:00] [16:05:00.048] Removed 55999 Traits
[INFO] [2021-04-03 16:05:00] ## remove_type: MetaTrait
[INFO] [2021-04-03 16:05:00] ++ Calling delete_all on 111998 instances...
[INFO] [2021-04-03 16:05:05] [16:05:05.318] Removed 111998 Metatraits
[INFO] [2021-04-03 16:05:05] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-03 16:05:05] ++ Calling delete_all on 108605 instances...
[INFO] [2021-04-03 16:05:09] [16:05:09.900] Removed 108605 Occurrencemetadata
[INFO] [2021-04-03 16:05:09] ## remove_type: Assoc
[INFO] [2021-04-03 16:05:09] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-03 16:05:09] [16:05:09.902] Removed 0 Assocs
[INFO] [2021-04-03 16:05:09] ## remove_type: MetaAssoc
[INFO] [2021-04-03 16:05:09] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-03 16:05:09] [16:05:09.903] Removed 0 Metaassocs
[INFO] [2021-04-03 16:05:09] ## remove_type: Identifier
[INFO] [2021-04-03 16:05:09] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-03 16:05:09] [16:05:09.905] Removed 0 Identifiers
[INFO] [2021-04-03 16:05:09] ## remove_type: Reference
[INFO] [2021-04-03 16:05:09] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-03 16:05:09] [16:05:09.906] Removed 0 References
[INFO] [2021-04-03 16:05:10] Starting batch with ID 87669022...
[INFO] [2021-04-03 16:05:11] Starting batch with ID 87660729...
[INFO] [2021-04-03 16:05:11] Starting batch with ID 87660729...
[INFO] [2021-04-03 16:05:12] Starting batch with ID 87660729...
[INFO] [2021-04-03 16:05:12] Starting batch with ID 87668366...
[INFO] [2021-04-03 16:05:13] Starting batch with ID 87668366...
[INFO] [2021-04-03 16:05:13] Starting batch with ID 87664481...
[INFO] [2021-04-03 16:05:13] Starting batch with ID 87664481...
[INFO] [2021-04-03 16:05:13] Starting batch with ID 87664481...
[INFO] [2021-04-03 16:05:13] Starting batch with ID 87664481...
[INFO] [2021-04-03 16:05:13] Starting batch with ID 87664481...
[INFO] [2021-04-03 16:05:13] Starting batch with ID 87664481...
[INFO] [2021-04-03 16:05:13] Starting batch with ID 87664481...
[INFO] [2021-04-03 16:05:13] Starting batch with ID 87664481...
[INFO] [2021-04-03 16:05:13] Starting batch with ID 87664481...
[INFO] [2021-04-03 16:05:13] Starting batch with ID 87664481...
[INFO] [2021-04-03 16:05:14] Starting batch with ID 87664481...
[INFO] [2021-04-03 16:05:14] Starting batch with ID 87664481...
[INFO] [2021-04-03 16:05:14] ## remove_type: Node
[INFO] [2021-04-03 16:05:14] ++ Calling delete_all on 15532 instances...
[INFO] [2021-04-03 16:05:14] [16:05:14.929] Removed 15532 Nodes
[START] [2021-04-03 16:05:19] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-03 16:05:19] Creating resource from OpenData
[START] [2021-04-03 16:05:21] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-03 16:05:21] Parse meta.xml file and create formats with fields
[WARN] [2021-04-03 16:05:28] (common) IGNORED (occurrences) field header: eventID term: http://rs.tdwg.org/dwc/terms/eventID
[STOP] [2021-04-03 16:05:28] Parse meta.xml file and create formats with fields
[STOP] [2021-04-03 16:05:28] Creating resource from OpenData
[START] [2021-04-03 16:05:29] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-03 16:05:29] create_harvest_instance
[INFO] [2021-04-03 16:05:29] Created harvest instance #3602
[STOP] [2021-04-03 16:05:29] create_harvest_instance
[START] [2021-04-03 16:05:29] fetch_files
[STOP] [2021-04-03 16:05:29] fetch_files
[START] [2021-04-03 16:05:29] validate_each_file
[INFO] [2021-04-03 16:05:29] Looping over 3 formats...
[INFO] [2021-04-03 16:05:29] ...nodes (/app/public/data/NMNHGrowthForm/taxon.tab)
[INFO] [2021-04-03 16:05:30] Valid: /app/public/converted_csv/NMNHGrowthForm_nodes_3602.csv (12698 lines)
[INFO] [2021-04-03 16:05:30] ...occurrences (/app/public/data/NMNHGrowthForm/occurrence_specific.tab)
[INFO] [2021-04-03 16:05:35] Valid: /app/public/converted_csv/NMNHGrowthForm_occurrences_3602.csv (55999 lines)
[INFO] [2021-04-03 16:05:35] ...measurements (/app/public/data/NMNHGrowthForm/measurement_or_fact.tab)
[INFO] [2021-04-03 16:05:48] Valid: /app/public/converted_csv/NMNHGrowthForm_measurements_3602.csv (164604 lines)
[STOP] [2021-04-03 16:05:48] validate_each_file
[START] [2021-04-03 16:05:48] convert_to_csv
[INFO] [2021-04-03 16:05:48] Looping over 3 formats...
[INFO] [2021-04-03 16:05:48] ...nodes (/app/public/data/NMNHGrowthForm/taxon.tab)
[CMD] [2021-04-03 16:05:48] /usr/bin/sort /app/public/converted_csv/NMNHGrowthForm_nodes_3602.csv > /app/public/converted_csv/NMNHGrowthForm_nodes_3602.csv_sorted
[INFO] [2021-04-03 16:05:48] Converted: /app/public/converted_csv/NMNHGrowthForm_nodes_3602.csv (12698 lines)
[INFO] [2021-04-03 16:05:48] ...occurrences (/app/public/data/NMNHGrowthForm/occurrence_specific.tab)
[CMD] [2021-04-03 16:05:48] /usr/bin/sort /app/public/converted_csv/NMNHGrowthForm_occurrences_3602.csv > /app/public/converted_csv/NMNHGrowthForm_occurrences_3602.csv_sorted
[INFO] [2021-04-03 16:05:49] Converted: /app/public/converted_csv/NMNHGrowthForm_occurrences_3602.csv (55999 lines)
[INFO] [2021-04-03 16:05:49] ...measurements (/app/public/data/NMNHGrowthForm/measurement_or_fact.tab)
[CMD] [2021-04-03 16:05:49] /usr/bin/sort /app/public/converted_csv/NMNHGrowthForm_measurements_3602.csv > /app/public/converted_csv/NMNHGrowthForm_measurements_3602.csv_sorted
[INFO] [2021-04-03 16:05:50] Converted: /app/public/converted_csv/NMNHGrowthForm_measurements_3602.csv (164604 lines)
[STOP] [2021-04-03 16:05:50] convert_to_csv
[START] [2021-04-03 16:05:50] calculate_delta
[INFO] [2021-04-03 16:05:50] Looping over 3 formats...
[INFO] [2021-04-03 16:05:50] ...nodes (/app/public/data/NMNHGrowthForm/taxon.tab)
[CMD] [2021-04-03 16:05:50] echo "0a" > /app/public/diff/NMNHGrowthForm_nodes_3602.diff
[CMD] [2021-04-03 16:05:51] tail -n +1 /app/public/converted_csv/NMNHGrowthForm_nodes_3602.csv >> /app/public/diff/NMNHGrowthForm_nodes_3602.diff
[CMD] [2021-04-03 16:05:52] echo "." >> /app/public/diff/NMNHGrowthForm_nodes_3602.diff
[INFO] [2021-04-03 16:05:52] Created diff: /app/public/diff/NMNHGrowthForm_nodes_3602.diff (12700 lines)
[INFO] [2021-04-03 16:05:52] ...occurrences (/app/public/data/NMNHGrowthForm/occurrence_specific.tab)
[CMD] [2021-04-03 16:05:52] echo "0a" > /app/public/diff/NMNHGrowthForm_occurrences_3602.diff
[CMD] [2021-04-03 16:05:53] tail -n +1 /app/public/converted_csv/NMNHGrowthForm_occurrences_3602.csv >> /app/public/diff/NMNHGrowthForm_occurrences_3602.diff
[CMD] [2021-04-03 16:05:54] echo "." >> /app/public/diff/NMNHGrowthForm_occurrences_3602.diff
[INFO] [2021-04-03 16:05:55] Created diff: /app/public/diff/NMNHGrowthForm_occurrences_3602.diff (56001 lines)
[INFO] [2021-04-03 16:05:55] ...measurements (/app/public/data/NMNHGrowthForm/measurement_or_fact.tab)
[CMD] [2021-04-03 16:05:55] echo "0a" > /app/public/diff/NMNHGrowthForm_measurements_3602.diff
[CMD] [2021-04-03 16:05:55] tail -n +1 /app/public/converted_csv/NMNHGrowthForm_measurements_3602.csv >> /app/public/diff/NMNHGrowthForm_measurements_3602.diff
[CMD] [2021-04-03 16:05:56] echo "." >> /app/public/diff/NMNHGrowthForm_measurements_3602.diff
[INFO] [2021-04-03 16:05:57] Created diff: /app/public/diff/NMNHGrowthForm_measurements_3602.diff (164606 lines)
[STOP] [2021-04-03 16:05:57] calculate_delta
[START] [2021-04-03 16:05:57] parse_diff_and_store
[INFO] [2021-04-03 16:05:57] Handling diff: /app/public/diff/NMNHGrowthForm_nodes_3602.diff (12700 lines)
[INFO] [2021-04-03 16:05:58] Loading nodes diff file into memory (12700 /app/public/diff/NMNHGrowthForm_nodes_3602.diff lines)...
[WARN] [2021-04-03 16:05:59] Filtered Scientific Name `Astilbe rubra Hook. f. & ex Hook.` to `Astilbe rubra Hook. f. & ex Hook.`
[WARN] [2021-04-03 16:06:02] Filtered Scientific Name `Schwenckia elegans Carvalho` to `Schwenckia elegans Carvalho`
[WARN] [2021-04-03 16:06:02] Filtered Scientific Name `Solanum davidsei Carvalho` to `Solanum davidsei Carvalho`
[INFO] [2021-04-03 16:06:03] Handling diff: /app/public/diff/NMNHGrowthForm_occurrences_3602.diff (56001 lines)
[INFO] [2021-04-03 16:06:04] Loading occurrences diff file into memory (56001 /app/public/diff/NMNHGrowthForm_occurrences_3602.diff lines)...
[INFO] [2021-04-03 16:06:11] Handling diff: /app/public/diff/NMNHGrowthForm_measurements_3602.diff (164606 lines)
[INFO] [2021-04-03 16:06:12] Loading measurements diff file into memory (164606 /app/public/diff/NMNHGrowthForm_measurements_3602.diff lines)...
[INFO] [2021-04-03 16:07:07] Storing 15532 ScientificNames
[INFO] [2021-04-03 16:07:07] Processing group of 15532 in 16 groups of 1000
[INFO] [2021-04-03 16:07:13] Average Time: 0.361
[INFO] [2021-04-03 16:07:13] Total Time: 6s
[INFO] [2021-04-03 16:07:13] last 3 / first 3: 0.31
[INFO] [2021-04-03 16:07:13] Std.Dev: 0.22803508501982758; Max: 0.95
[INFO] [2021-04-03 16:07:13] Storing 15532 Nodes
[INFO] [2021-04-03 16:07:13] Processing group of 15532 in 16 groups of 1000
[INFO] [2021-04-03 16:07:17] Average Time: 0.254
[INFO] [2021-04-03 16:07:17] Total Time: 5s
[INFO] [2021-04-03 16:07:17] last 3 / first 3: 0.76
[INFO] [2021-04-03 16:07:17] Std.Dev: 0.044721359549995794; Max: 0.34
[INFO] [2021-04-03 16:07:17] Storing 55999 Occurrences
[INFO] [2021-04-03 16:07:17] Processing group of 55999 in 56 groups of 1000
[INFO] [2021-04-03 16:07:23] Average Time: 0.108
[INFO] [2021-04-03 16:07:23] Total Time: 7s
[INFO] [2021-04-03 16:07:23] last 3 / first 3: 1.37
[INFO] [2021-04-03 16:07:23] Std.Dev: 0.03162277660168379; Max: 0.21
[INFO] [2021-04-03 16:07:23] Storing 108605 OccurrenceMetadata
[INFO] [2021-04-03 16:07:23] Processing group of 108605 in 109 groups of 1000
[INFO] [2021-04-03 16:07:38] Average Time: 0.124
[INFO] [2021-04-03 16:07:38] Total Time: 15s
[INFO] [2021-04-03 16:07:38] last 3 / first 3: 1.21
[INFO] [2021-04-03 16:07:38] Std.Dev: 0.044721359549995794; Max: 0.48
[INFO] [2021-04-03 16:07:38] Storing 55999 Traits
[INFO] [2021-04-03 16:07:38] Processing group of 55999 in 56 groups of 1000
[INFO] [2021-04-03 16:07:56] Average Time: 0.317
[INFO] [2021-04-03 16:07:56] Total Time: 18s
[INFO] [2021-04-03 16:07:56] last 3 / first 3: 1.0
[INFO] [2021-04-03 16:07:56] Std.Dev: 0.15491933384829668; Max: 0.97
[INFO] [2021-04-03 16:07:56] Storing 111998 MetaTraits
[INFO] [2021-04-03 16:07:56] Processing group of 111998 in 112 groups of 1000
[INFO] [2021-04-03 16:08:09] Average Time: 0.116
[INFO] [2021-04-03 16:08:09] Total Time: 14s
[INFO] [2021-04-03 16:08:09] last 3 / first 3: 1.0
[INFO] [2021-04-03 16:08:09] Std.Dev: 0.0; Max: 0.19
[STOP] [2021-04-03 16:08:09] parse_diff_and_store
[START] [2021-04-03 16:08:09] resolve_keys
[INFO] [2021-04-03 16:08:17] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-03 16:08:21] traits to occurrences...
[INFO] [2021-04-03 16:08:22] traits to nodes (through occurrences)...
[INFO] [2021-04-03 16:08:23] Traits to sex term...
[INFO] [2021-04-03 16:08:24] Traits to lifestage term...
[INFO] [2021-04-03 16:08:25] MetaTraits to traits...
[INFO] [2021-04-03 16:08:27] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-03 16:08:27] Assocs to occurrences...
[INFO] [2021-04-03 16:08:27] Assocs to nodes...
[INFO] [2021-04-03 16:08:27] Assoc to sex term...
[INFO] [2021-04-03 16:08:27] Assoc to lifestage term...
[INFO] [2021-04-03 16:08:27] MetaAssoc to assocs...
[STOP] [2021-04-03 16:08:27] resolve_keys
[START] [2021-04-03 16:08:27] hold_for_later_1
[STOP] [2021-04-03 16:08:27] hold_for_later_1
[START] [2021-04-03 16:08:27] hold_for_later_2
[STOP] [2021-04-03 16:08:27] hold_for_later_2
[START] [2021-04-03 16:08:27] resolve_missing_parents
[STOP] [2021-04-03 16:08:28] resolve_missing_parents
[START] [2021-04-03 16:08:28] rebuild_nodes
[START] [2021-04-03 16:08:28] Flattener#flatten
[START] [2021-04-03 16:08:28] Flattener#study_resource
[START] [2021-04-03 16:08:28] Flattener#build_ancestry
[STOP] [2021-04-03 16:08:31] Flattener#build_ancestry
[INFO] [2021-04-03 16:08:31] 15532 ancestry keys
[START] [2021-04-03 16:08:31] build_node_ancestors
[INFO] [2021-04-03 16:08:31] old ancestors deleted.
[STOP] [2021-04-03 16:08:31] build_node_ancestors
[START] [2021-04-03 16:08:32] Flattener#propagate_ancestor_ids
[STOP] [2021-04-03 16:08:32] Flattener#propagate_ancestor_ids
[STOP] [2021-04-03 16:08:32] Flattener#flatten
[STOP] [2021-04-03 16:08:32] rebuild_nodes
[START] [2021-04-03 16:08:32] resolve_missing_media_owners
[STOP] [2021-04-03 16:08:32] resolve_missing_media_owners
[START] [2021-04-03 16:08:32] sanitize_media_verbatims
[STOP] [2021-04-03 16:08:32] sanitize_media_verbatims
[START] [2021-04-03 16:08:32] queue_downloads
[STOP] [2021-04-03 16:08:32] queue_downloads
[START] [2021-04-03 16:08:32] parse_names
[WARN] [2021-04-03 16:08:32] I see 15532 names which still need to be parsed.
[STOP] [2021-04-03 16:08:44] parse_names
[START] [2021-04-03 16:08:44] denormalize_canonical_names_to_nodes
[STOP] [2021-04-03 16:08:44] denormalize_canonical_names_to_nodes
[START] [2021-04-03 16:08:44] match_nodes
[START] [2021-04-03 16:08:44] map_all_nodes_to_pages
[STOP] [2021-04-03 16:11:42] map_all_nodes_to_pages
[INFO] [2021-04-03 16:11:42] 1506 Unmatched nodes (of 15532)! That's too many to output. Full list in /app/public/data/NMNHGrowthForm/unmatched_nodes.txt ; First 10: Abarema aspleniifolia (#91431771); Abarema mataybifolia (#91431776); Abelmoschus moschatus (#91431785); Abies ernestii salouensis (#91431787); Abildgaardia (#91431795); Abroma (#91431799); Abroma augustum (#91431800); Abutilon sandwicense (#91431818); Acacia angulosa (#91431823); Acacia angustissima angustissima (#91431825)
[START] [2021-04-03 16:11:42] update_nodes
[STOP] [2021-04-03 16:11:47] update_nodes
[STOP] [2021-04-03 16:11:47] match_nodes
[START] [2021-04-03 16:11:47] reindex_search
[STOP] [2021-04-03 16:11:57] reindex_search
[START] [2021-04-03 16:11:57] normalize_units
[STOP] [2021-04-03 16:11:57] normalize_units
[START] [2021-04-03 16:11:57] calculate_statistics
[STOP] [2021-04-03 16:11:58] calculate_statistics
[START] [2021-04-03 16:11:58] complete_harvest_instance
[START] [2021-04-03 16:11:58] overall_tsv_creation
[INFO] [2021-04-03 16:11:58] Processing group of 15532 in 2 batches of 10000
[INFO] [2021-04-03 16:13:03] 34956 Traits (unfiltered)...
[INFO] [2021-04-03 16:17:17] 34956 Traits (filtered)...
[INFO] [2021-04-03 16:17:20] 0 Associations (filtered)...
[INFO] [2021-04-03 16:17:30] 68015 metadata added.
[INFO] [2021-04-03 16:17:30] 0 metadata added.
[INFO] [2021-04-03 16:18:56] 21043 Traits (unfiltered)...
[INFO] [2021-04-03 16:21:46] 21043 Traits (filtered)...
[INFO] [2021-04-03 16:21:48] 0 Associations (filtered)...
[INFO] [2021-04-03 16:21:56] 40590 metadata added.
[INFO] [2021-04-03 16:21:56] 0 metadata added.
[INFO] [2021-04-03 16:22:25] Average Time: 286.08
[INFO] [2021-04-03 16:22:25] Total Time: 10m28s
[STOP] [2021-04-03 16:22:25] overall_tsv_creation
[INFO] [2021-04-03 16:22:25] Done. Check your files:
[INFO] [2021-04-03 16:22:26] (15532 lines) /app/public/data/NMNHGrowthForm/publish_nodes.tsv
[INFO] [2021-04-03 16:22:27] (12698 lines) /app/public/data/NMNHGrowthForm/publish_node_ancestors.tsv
[INFO] [2021-04-03 16:22:27] (15532 lines) /app/public/data/NMNHGrowthForm/publish_scientific_names.tsv
[INFO] [2021-04-03 16:22:28] (56000 lines) /app/public/data/NMNHGrowthForm/publish_traits.tsv
[INFO] [2021-04-03 16:22:29] (108606 lines) /app/public/data/NMNHGrowthForm/publish_metadata.tsv
[STOP] [2021-04-03 16:22:29] complete_harvest_instance
[START] [2021-04-03 16:22:29] completed
[STOP] [2021-04-03 16:22:29] completed
[STOP] [2021-04-03 16:22:29] logged process, took 1021.05
Latest Process