Harvest for Ullrich-L├╝ter et al 2011 Created 19 Apr 15:25

Stage: completed
Fetched: 19 Apr 15:25
Validated: 19 Apr 15:25
Deltas Created 19 Apr 15:25
Units Normalized: 19 Apr 15:25
Ancestry Built: 19 Apr 15:25
Nodes Matched: 19 Apr 15:25
Names Parsed: 19 Apr 15:25
New Models Stored: 19 Apr 15:25
Indexed: 19 Apr 15:25
Completed: 19 Apr 15:26
Time to Harvest: less than a minute

Harvesting Log

(491 lines)
# Logfile created on 2020-08-27 15:39:48 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:39:48] logged process
[START] [2020-08-27 15:39:48] Creating resource from OpenData
[START] [2020-08-27 15:39:48] logged process
[START] [2020-08-27 15:39:48] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:39:48] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:39:48] Creating resource from OpenData
[INFO] [2020-11-19 14:15:03] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 14:15:05] ## remove_type: ScientificName
[INFO] [2020-11-19 14:15:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:15:05] [14:15:05.936] Removed 0 Scientificnames
[INFO] [2020-11-19 14:15:05] ## remove_type: Vernacular
[INFO] [2020-11-19 14:15:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:15:05] [14:15:05.938] Removed 0 Vernaculars
[INFO] [2020-11-19 14:15:05] ## remove_type: Article
[INFO] [2020-11-19 14:15:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:15:05] [14:15:05.941] Removed 0 Articles
[INFO] [2020-11-19 14:15:05] ## remove_type: Medium
[INFO] [2020-11-19 14:15:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:15:05] [14:15:05.944] Removed 0 Media
[INFO] [2020-11-19 14:15:05] ## remove_type: Trait
[INFO] [2020-11-19 14:15:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:15:05] [14:15:05.947] Removed 0 Traits
[INFO] [2020-11-19 14:15:05] ## remove_type: MetaTrait
[INFO] [2020-11-19 14:15:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:15:05] [14:15:05.950] Removed 0 Metatraits
[INFO] [2020-11-19 14:15:05] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 14:15:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:15:05] [14:15:05.952] Removed 0 Occurrencemetadata
[INFO] [2020-11-19 14:15:05] ## remove_type: Assoc
[INFO] [2020-11-19 14:15:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:15:05] [14:15:05.955] Removed 0 Assocs
[INFO] [2020-11-19 14:15:05] ## remove_type: MetaAssoc
[INFO] [2020-11-19 14:15:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:15:05] [14:15:05.958] Removed 0 Metaassocs
[INFO] [2020-11-19 14:15:05] ## remove_type: Identifier
[INFO] [2020-11-19 14:15:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:15:05] [14:15:05.960] Removed 0 Identifiers
[INFO] [2020-11-19 14:15:05] ## remove_type: Reference
[INFO] [2020-11-19 14:15:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:15:05] [14:15:05.962] Removed 0 References
[INFO] [2020-11-19 14:15:05] ## remove_type: Node
[INFO] [2020-11-19 14:15:05] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 14:15:05] [14:15:05.982] Removed 0 Nodes
[START] [2020-11-19 14:15:06] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 14:15:06] Creating resource from OpenData
[START] [2020-11-19 14:15:06] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 14:15:06] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 14:15:06] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 14:15:06] Creating resource from OpenData
[START] [2020-11-19 14:15:06] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 14:15:06] create_harvest_instance
[STOP] [2020-11-19 14:15:07] create_harvest_instance
[START] [2020-11-19 14:15:07] fetch_files
[STOP] [2020-11-19 14:15:07] fetch_files
[START] [2020-11-19 14:15:07] validate_each_file
[STOP] [2020-11-19 14:15:08] validate_each_file
[START] [2020-11-19 14:15:08] convert_to_csv
[CMD] [2020-11-19 14:15:08] /usr/bin/sort /app/public/converted_csv/uuteau_refs_24558.csv > /app/public/converted_csv/uuteau_refs_24558.csv_sorted
[CMD] [2020-11-19 14:15:08] /usr/bin/sort /app/public/converted_csv/uuteau_nodes_24559.csv > /app/public/converted_csv/uuteau_nodes_24559.csv_sorted
[CMD] [2020-11-19 14:15:08] /usr/bin/sort /app/public/converted_csv/uuteau_occurrences_24560.csv > /app/public/converted_csv/uuteau_occurrences_24560.csv_sorted
[CMD] [2020-11-19 14:15:08] /usr/bin/sort /app/public/converted_csv/uuteau_measurements_24561.csv > /app/public/converted_csv/uuteau_measurements_24561.csv_sorted
[STOP] [2020-11-19 14:15:08] convert_to_csv
[START] [2020-11-19 14:15:08] calculate_delta
[CMD] [2020-11-19 14:15:08] echo "0a" > /app/public/diff/uuteau_refs_24558.diff
[CMD] [2020-11-19 14:15:08] tail -n +1 /app/public/converted_csv/uuteau_refs_24558.csv >> /app/public/diff/uuteau_refs_24558.diff
[CMD] [2020-11-19 14:15:08] echo "." >> /app/public/diff/uuteau_refs_24558.diff
[CMD] [2020-11-19 14:15:08] echo "0a" > /app/public/diff/uuteau_nodes_24559.diff
[CMD] [2020-11-19 14:15:08] tail -n +1 /app/public/converted_csv/uuteau_nodes_24559.csv >> /app/public/diff/uuteau_nodes_24559.diff
[CMD] [2020-11-19 14:15:08] echo "." >> /app/public/diff/uuteau_nodes_24559.diff
[CMD] [2020-11-19 14:15:08] echo "0a" > /app/public/diff/uuteau_occurrences_24560.diff
[CMD] [2020-11-19 14:15:08] tail -n +1 /app/public/converted_csv/uuteau_occurrences_24560.csv >> /app/public/diff/uuteau_occurrences_24560.diff
[CMD] [2020-11-19 14:15:08] echo "." >> /app/public/diff/uuteau_occurrences_24560.diff
[CMD] [2020-11-19 14:15:08] echo "0a" > /app/public/diff/uuteau_measurements_24561.diff
[CMD] [2020-11-19 14:15:08] tail -n +1 /app/public/converted_csv/uuteau_measurements_24561.csv >> /app/public/diff/uuteau_measurements_24561.diff
[CMD] [2020-11-19 14:15:08] echo "." >> /app/public/diff/uuteau_measurements_24561.diff
[STOP] [2020-11-19 14:15:08] calculate_delta
[START] [2020-11-19 14:15:08] parse_diff_and_store
[INFO] [2020-11-19 14:15:08] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 14:15:08] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 14:15:08] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 14:15:08] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-19 14:15:09] Storing 1 ScientificNames
[INFO] [2020-11-19 14:15:09] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 14:15:09] Average Time: 0.0
[INFO] [2020-11-19 14:15:09] Total Time: 1s
[INFO] [2020-11-19 14:15:09] Storing 1 Nodes
[INFO] [2020-11-19 14:15:09] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 14:15:09] Average Time: 0.0
[INFO] [2020-11-19 14:15:09] Total Time: 1s
[INFO] [2020-11-19 14:15:09] Storing 1 Occurrences
[INFO] [2020-11-19 14:15:09] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 14:15:09] Average Time: 0.0
[INFO] [2020-11-19 14:15:09] Total Time: 1s
[INFO] [2020-11-19 14:15:09] Storing 3 Traits
[INFO] [2020-11-19 14:15:09] Processing group of 3 in 1 groups of 1000
[INFO] [2020-11-19 14:15:09] Average Time: 0.0
[INFO] [2020-11-19 14:15:09] Total Time: 1s
[INFO] [2020-11-19 14:15:09] Storing 2 MetaTraits
[INFO] [2020-11-19 14:15:09] Processing group of 2 in 1 groups of 1000
[INFO] [2020-11-19 14:15:09] Average Time: 0.0
[INFO] [2020-11-19 14:15:09] Total Time: 1s
[STOP] [2020-11-19 14:15:09] parse_diff_and_store
[START] [2020-11-19 14:15:09] resolve_keys
[INFO] [2020-11-19 14:15:15] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-19 14:15:15] traits to occurrences...
[INFO] [2020-11-19 14:15:15] traits to nodes (through occurrences)...
[INFO] [2020-11-19 14:15:15] Traits to sex term...
[INFO] [2020-11-19 14:15:15] Traits to lifestage term...
[INFO] [2020-11-19 14:15:15] MetaTraits to traits...
[INFO] [2020-11-19 14:15:15] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-19 14:15:15] Assocs to occurrences...
[INFO] [2020-11-19 14:15:15] Assocs to nodes...
[INFO] [2020-11-19 14:15:15] Assoc to sex term...
[INFO] [2020-11-19 14:15:15] Assoc to lifestage term...
[INFO] [2020-11-19 14:15:15] MetaAssoc to assocs...
[STOP] [2020-11-19 14:15:15] resolve_keys
[START] [2020-11-19 14:15:15] hold_for_later_1
[STOP] [2020-11-19 14:15:15] hold_for_later_1
[START] [2020-11-19 14:15:15] hold_for_later_2
[STOP] [2020-11-19 14:15:15] hold_for_later_2
[START] [2020-11-19 14:15:15] resolve_missing_parents
[STOP] [2020-11-19 14:15:15] resolve_missing_parents
[START] [2020-11-19 14:15:15] rebuild_nodes
[START] [2020-11-19 14:15:15] Flattener#flatten
[START] [2020-11-19 14:15:15] Flattener#study_resource
[START] [2020-11-19 14:15:15] Flattener#build_ancestry
[STOP] [2020-11-19 14:15:15] Flattener#build_ancestry
[INFO] [2020-11-19 14:15:15] 1 ancestry keys
[START] [2020-11-19 14:15:15] build_node_ancestors
[INFO] [2020-11-19 14:15:15] old ancestors deleted.
[STOP] [2020-11-19 14:15:15] build_node_ancestors
[WARN] [2020-11-19 14:15:15] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-19 14:15:15] Flattener#flatten
[STOP] [2020-11-19 14:15:15] rebuild_nodes
[START] [2020-11-19 14:15:15] resolve_missing_media_owners
[STOP] [2020-11-19 14:15:15] resolve_missing_media_owners
[START] [2020-11-19 14:15:15] sanitize_media_verbatims
[STOP] [2020-11-19 14:15:15] sanitize_media_verbatims
[START] [2020-11-19 14:15:15] queue_downloads
[STOP] [2020-11-19 14:15:15] queue_downloads
[START] [2020-11-19 14:15:15] parse_names
[WARN] [2020-11-19 14:15:15] I see 1 names which still need to be parsed.
[STOP] [2020-11-19 14:15:16] parse_names
[START] [2020-11-19 14:15:16] denormalize_canonical_names_to_nodes
[STOP] [2020-11-19 14:15:16] denormalize_canonical_names_to_nodes
[START] [2020-11-19 14:15:16] match_nodes
[START] [2020-11-19 14:15:16] map_all_nodes_to_pages
[STOP] [2020-11-19 14:15:16] map_all_nodes_to_pages
[INFO] [2020-11-19 14:15:16] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-11-19 14:15:16] update_nodes
[STOP] [2020-11-19 14:15:16] update_nodes
[STOP] [2020-11-19 14:15:16] match_nodes
[START] [2020-11-19 14:15:16] reindex_search
[STOP] [2020-11-19 14:15:16] reindex_search
[START] [2020-11-19 14:15:16] normalize_units
[STOP] [2020-11-19 14:15:16] normalize_units
[START] [2020-11-19 14:15:16] calculate_statistics
[2020-11-19 14:15:16] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-19 14:15:16] calculate_statistics
[START] [2020-11-19 14:15:16] complete_harvest_instance
[START] [2020-11-19 14:15:16] overall_tsv_creation
[INFO] [2020-11-19 14:15:16] Processing group of 1 in 1 batches of 10000
[INFO] [2020-11-19 14:15:59] 1 Traits (unfiltered)...
[INFO] [2020-11-19 14:16:42] 1 Traits (filtered)...
[INFO] [2020-11-19 14:16:42] 0 Associations (filtered)...
[INFO] [2020-11-19 14:16:42] 4 metadata added.
[INFO] [2020-11-19 14:16:42] 0 metadata added.
[INFO] [2020-11-19 14:16:42] Average Time: 66.49
[INFO] [2020-11-19 14:16:42] Total Time: 1m27s
[STOP] [2020-11-19 14:16:42] overall_tsv_creation
[INFO] [2020-11-19 14:16:42] Done. Check your files:
[INFO] [2020-11-19 14:16:42] (1 lines) /app/public/data/uuteau/publish_nodes.tsv
[INFO] [2020-11-19 14:16:42] (1 lines) /app/public/data/uuteau/publish_scientific_names.tsv
[INFO] [2020-11-19 14:16:42] (2 lines) /app/public/data/uuteau/publish_traits.tsv
[INFO] [2020-11-19 14:16:42] (5 lines) /app/public/data/uuteau/publish_metadata.tsv
[STOP] [2020-11-19 14:16:42] complete_harvest_instance
[START] [2020-11-19 14:16:42] completed
[STOP] [2020-11-19 14:16:42] completed
[STOP] [2020-11-19 14:16:42] logged process, took 96.5
[INFO] [2021-04-19 15:16:11] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:24:58] ## remove_type: ScientificName
[INFO] [2021-04-19 15:24:58] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:24:58] [15:24:58.995] Removed 1 Scientificnames
[INFO] [2021-04-19 15:24:58] ## remove_type: Vernacular
[INFO] [2021-04-19 15:24:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:24:58] [15:24:58.997] Removed 0 Vernaculars
[INFO] [2021-04-19 15:24:58] ## remove_type: Article
[INFO] [2021-04-19 15:24:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:24:58] [15:24:58.999] Removed 0 Articles
[INFO] [2021-04-19 15:24:58] ## remove_type: Medium
[INFO] [2021-04-19 15:24:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:24:59] [15:24:59.001] Removed 0 Media
[INFO] [2021-04-19 15:24:59] ## remove_type: Trait
[INFO] [2021-04-19 15:24:59] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 15:24:59] [15:24:59.003] Removed 3 Traits
[INFO] [2021-04-19 15:24:59] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:24:59] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:24:59] [15:24:59.005] Removed 2 Metatraits
[INFO] [2021-04-19 15:24:59] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:24:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:24:59] [15:24:59.006] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:24:59] ## remove_type: Assoc
[INFO] [2021-04-19 15:24:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:24:59] [15:24:59.008] Removed 0 Assocs
[INFO] [2021-04-19 15:24:59] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:24:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:24:59] [15:24:59.009] Removed 0 Metaassocs
[INFO] [2021-04-19 15:24:59] ## remove_type: Identifier
[INFO] [2021-04-19 15:24:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:24:59] [15:24:59.011] Removed 0 Identifiers
[INFO] [2021-04-19 15:24:59] ## remove_type: Reference
[INFO] [2021-04-19 15:24:59] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:24:59] [15:24:59.013] Removed 0 References
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] Starting batch with ID 84620952...
[INFO] [2021-04-19 15:24:59] ## remove_type: Node
[INFO] [2021-04-19 15:24:59] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:24:59] [15:24:59.723] Removed 1 Nodes
[START] [2021-04-19 15:24:59] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:24:59] Creating resource from OpenData
[START] [2021-04-19 15:24:59] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:24:59] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:25:00] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:25:00] Creating resource from OpenData
[START] [2021-04-19 15:25:00] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:25:00] create_harvest_instance
[INFO] [2021-04-19 15:25:00] Created harvest instance #3765
[STOP] [2021-04-19 15:25:00] create_harvest_instance
[START] [2021-04-19 15:25:00] fetch_files
[STOP] [2021-04-19 15:25:00] fetch_files
[START] [2021-04-19 15:25:00] validate_each_file
[INFO] [2021-04-19 15:25:00] Looping over 4 formats...
[INFO] [2021-04-19 15:25:00] ...refs (/app/public/data/uuteau/references.tsv)
[INFO] [2021-04-19 15:25:00] Valid: /app/public/converted_csv/uuteau_refs_3765.csv (0 lines)
[INFO] [2021-04-19 15:25:00] ...nodes (/app/public/data/uuteau/taxa.txt)
[INFO] [2021-04-19 15:25:00] Valid: /app/public/converted_csv/uuteau_nodes_3765.csv (1 lines)
[INFO] [2021-04-19 15:25:00] ...occurrences (/app/public/data/uuteau/occurrences.txt)
[INFO] [2021-04-19 15:25:00] Valid: /app/public/converted_csv/uuteau_occurrences_3765.csv (1 lines)
[INFO] [2021-04-19 15:25:00] ...measurements (/app/public/data/uuteau/measurementsorfacts.txt)
[INFO] [2021-04-19 15:25:00] Valid: /app/public/converted_csv/uuteau_measurements_3765.csv (3 lines)
[STOP] [2021-04-19 15:25:00] validate_each_file
[START] [2021-04-19 15:25:00] convert_to_csv
[INFO] [2021-04-19 15:25:00] Looping over 4 formats...
[INFO] [2021-04-19 15:25:00] ...refs (/app/public/data/uuteau/references.tsv)
[CMD] [2021-04-19 15:25:00] /usr/bin/sort /app/public/converted_csv/uuteau_refs_3765.csv > /app/public/converted_csv/uuteau_refs_3765.csv_sorted
[INFO] [2021-04-19 15:25:00] Converted: /app/public/converted_csv/uuteau_refs_3765.csv (0 lines)
[INFO] [2021-04-19 15:25:00] ...nodes (/app/public/data/uuteau/taxa.txt)
[CMD] [2021-04-19 15:25:00] /usr/bin/sort /app/public/converted_csv/uuteau_nodes_3765.csv > /app/public/converted_csv/uuteau_nodes_3765.csv_sorted
[INFO] [2021-04-19 15:25:00] Converted: /app/public/converted_csv/uuteau_nodes_3765.csv (1 lines)
[INFO] [2021-04-19 15:25:00] ...occurrences (/app/public/data/uuteau/occurrences.txt)
[CMD] [2021-04-19 15:25:00] /usr/bin/sort /app/public/converted_csv/uuteau_occurrences_3765.csv > /app/public/converted_csv/uuteau_occurrences_3765.csv_sorted
[INFO] [2021-04-19 15:25:00] Converted: /app/public/converted_csv/uuteau_occurrences_3765.csv (1 lines)
[INFO] [2021-04-19 15:25:00] ...measurements (/app/public/data/uuteau/measurementsorfacts.txt)
[CMD] [2021-04-19 15:25:00] /usr/bin/sort /app/public/converted_csv/uuteau_measurements_3765.csv > /app/public/converted_csv/uuteau_measurements_3765.csv_sorted
[INFO] [2021-04-19 15:25:00] Converted: /app/public/converted_csv/uuteau_measurements_3765.csv (3 lines)
[STOP] [2021-04-19 15:25:00] convert_to_csv
[START] [2021-04-19 15:25:00] calculate_delta
[INFO] [2021-04-19 15:25:00] Looping over 4 formats...
[INFO] [2021-04-19 15:25:00] ...refs (/app/public/data/uuteau/references.tsv)
[CMD] [2021-04-19 15:25:00] echo "0a" > /app/public/diff/uuteau_refs_3765.diff
[CMD] [2021-04-19 15:25:00] tail -n +1 /app/public/converted_csv/uuteau_refs_3765.csv >> /app/public/diff/uuteau_refs_3765.diff
[CMD] [2021-04-19 15:25:00] echo "." >> /app/public/diff/uuteau_refs_3765.diff
[INFO] [2021-04-19 15:25:00] Created diff: /app/public/diff/uuteau_refs_3765.diff (2 lines)
[INFO] [2021-04-19 15:25:00] ...nodes (/app/public/data/uuteau/taxa.txt)
[CMD] [2021-04-19 15:25:00] echo "0a" > /app/public/diff/uuteau_nodes_3765.diff
[CMD] [2021-04-19 15:25:00] tail -n +1 /app/public/converted_csv/uuteau_nodes_3765.csv >> /app/public/diff/uuteau_nodes_3765.diff
[CMD] [2021-04-19 15:25:00] echo "." >> /app/public/diff/uuteau_nodes_3765.diff
[INFO] [2021-04-19 15:25:00] Created diff: /app/public/diff/uuteau_nodes_3765.diff (3 lines)
[INFO] [2021-04-19 15:25:00] ...occurrences (/app/public/data/uuteau/occurrences.txt)
[CMD] [2021-04-19 15:25:00] echo "0a" > /app/public/diff/uuteau_occurrences_3765.diff
[CMD] [2021-04-19 15:25:00] tail -n +1 /app/public/converted_csv/uuteau_occurrences_3765.csv >> /app/public/diff/uuteau_occurrences_3765.diff
[CMD] [2021-04-19 15:25:00] echo "." >> /app/public/diff/uuteau_occurrences_3765.diff
[INFO] [2021-04-19 15:25:00] Created diff: /app/public/diff/uuteau_occurrences_3765.diff (3 lines)
[INFO] [2021-04-19 15:25:00] ...measurements (/app/public/data/uuteau/measurementsorfacts.txt)
[CMD] [2021-04-19 15:25:00] echo "0a" > /app/public/diff/uuteau_measurements_3765.diff
[CMD] [2021-04-19 15:25:00] tail -n +1 /app/public/converted_csv/uuteau_measurements_3765.csv >> /app/public/diff/uuteau_measurements_3765.diff
[CMD] [2021-04-19 15:25:00] echo "." >> /app/public/diff/uuteau_measurements_3765.diff
[INFO] [2021-04-19 15:25:00] Created diff: /app/public/diff/uuteau_measurements_3765.diff (5 lines)
[STOP] [2021-04-19 15:25:00] calculate_delta
[START] [2021-04-19 15:25:00] parse_diff_and_store
[INFO] [2021-04-19 15:25:00] Handling diff: /app/public/diff/uuteau_refs_3765.diff (2 lines)
[INFO] [2021-04-19 15:25:00] Loading refs diff file into memory (2 /app/public/diff/uuteau_refs_3765.diff lines)...
[INFO] [2021-04-19 15:25:00] Handling diff: /app/public/diff/uuteau_nodes_3765.diff (3 lines)
[INFO] [2021-04-19 15:25:00] Loading nodes diff file into memory (3 /app/public/diff/uuteau_nodes_3765.diff lines)...
[INFO] [2021-04-19 15:25:00] Handling diff: /app/public/diff/uuteau_occurrences_3765.diff (3 lines)
[INFO] [2021-04-19 15:25:00] Loading occurrences diff file into memory (3 /app/public/diff/uuteau_occurrences_3765.diff lines)...
[INFO] [2021-04-19 15:25:00] Handling diff: /app/public/diff/uuteau_measurements_3765.diff (5 lines)
[INFO] [2021-04-19 15:25:00] Loading measurements diff file into memory (5 /app/public/diff/uuteau_measurements_3765.diff lines)...
[INFO] [2021-04-19 15:25:00] Storing 1 ScientificNames
[INFO] [2021-04-19 15:25:00] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:25:00] Average Time: 0.0
[INFO] [2021-04-19 15:25:00] Total Time: 1s
[INFO] [2021-04-19 15:25:00] Storing 1 Nodes
[INFO] [2021-04-19 15:25:00] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:25:00] Average Time: 0.0
[INFO] [2021-04-19 15:25:00] Total Time: 1s
[INFO] [2021-04-19 15:25:00] Storing 1 Occurrences
[INFO] [2021-04-19 15:25:00] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:25:00] Average Time: 0.0
[INFO] [2021-04-19 15:25:00] Total Time: 1s
[INFO] [2021-04-19 15:25:00] Storing 3 Traits
[INFO] [2021-04-19 15:25:00] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 15:25:00] Average Time: 0.0
[INFO] [2021-04-19 15:25:00] Total Time: 1s
[INFO] [2021-04-19 15:25:00] Storing 2 MetaTraits
[INFO] [2021-04-19 15:25:00] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:25:00] Average Time: 0.0
[INFO] [2021-04-19 15:25:00] Total Time: 1s
[STOP] [2021-04-19 15:25:00] parse_diff_and_store
[START] [2021-04-19 15:25:00] resolve_keys
[INFO] [2021-04-19 15:25:06] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:25:06] traits to occurrences...
[INFO] [2021-04-19 15:25:06] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:25:06] Traits to sex term...
[INFO] [2021-04-19 15:25:06] Traits to lifestage term...
[INFO] [2021-04-19 15:25:06] MetaTraits to traits...
[INFO] [2021-04-19 15:25:06] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:25:06] Assocs to occurrences...
[INFO] [2021-04-19 15:25:06] Assocs to nodes...
[INFO] [2021-04-19 15:25:06] Assoc to sex term...
[INFO] [2021-04-19 15:25:06] Assoc to lifestage term...
[INFO] [2021-04-19 15:25:06] MetaAssoc to assocs...
[STOP] [2021-04-19 15:25:06] resolve_keys
[START] [2021-04-19 15:25:06] hold_for_later_1
[STOP] [2021-04-19 15:25:06] hold_for_later_1
[START] [2021-04-19 15:25:06] hold_for_later_2
[STOP] [2021-04-19 15:25:06] hold_for_later_2
[START] [2021-04-19 15:25:06] resolve_missing_parents
[STOP] [2021-04-19 15:25:06] resolve_missing_parents
[START] [2021-04-19 15:25:06] rebuild_nodes
[START] [2021-04-19 15:25:06] Flattener#flatten
[START] [2021-04-19 15:25:06] Flattener#study_resource
[START] [2021-04-19 15:25:06] Flattener#build_ancestry
[STOP] [2021-04-19 15:25:06] Flattener#build_ancestry
[INFO] [2021-04-19 15:25:06] 1 ancestry keys
[START] [2021-04-19 15:25:06] build_node_ancestors
[INFO] [2021-04-19 15:25:06] old ancestors deleted.
[STOP] [2021-04-19 15:25:06] build_node_ancestors
[WARN] [2021-04-19 15:25:06] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:25:06] Flattener#flatten
[STOP] [2021-04-19 15:25:06] rebuild_nodes
[START] [2021-04-19 15:25:06] resolve_missing_media_owners
[STOP] [2021-04-19 15:25:06] resolve_missing_media_owners
[START] [2021-04-19 15:25:06] sanitize_media_verbatims
[STOP] [2021-04-19 15:25:06] sanitize_media_verbatims
[START] [2021-04-19 15:25:06] queue_downloads
[STOP] [2021-04-19 15:25:06] queue_downloads
[START] [2021-04-19 15:25:06] parse_names
[WARN] [2021-04-19 15:25:06] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 15:25:07] parse_names
[START] [2021-04-19 15:25:07] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:25:07] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:25:07] match_nodes
[START] [2021-04-19 15:25:07] map_all_nodes_to_pages
[STOP] [2021-04-19 15:25:07] map_all_nodes_to_pages
[INFO] [2021-04-19 15:25:07] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 15:25:07] update_nodes
[STOP] [2021-04-19 15:25:07] update_nodes
[STOP] [2021-04-19 15:25:07] match_nodes
[START] [2021-04-19 15:25:07] reindex_search
[STOP] [2021-04-19 15:25:07] reindex_search
[START] [2021-04-19 15:25:07] normalize_units
[STOP] [2021-04-19 15:25:07] normalize_units
[START] [2021-04-19 15:25:07] calculate_statistics
[2021-04-19 15:25:07] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:25:07] calculate_statistics
[START] [2021-04-19 15:25:07] complete_harvest_instance
[START] [2021-04-19 15:25:07] overall_tsv_creation
[INFO] [2021-04-19 15:25:07] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 15:25:43] 1 Traits (unfiltered)...
[INFO] [2021-04-19 15:26:15] 1 Traits (filtered)...
[INFO] [2021-04-19 15:26:15] 0 Associations (filtered)...
[INFO] [2021-04-19 15:26:15] 2 metadata added.
[INFO] [2021-04-19 15:26:15] 0 metadata added.
[INFO] [2021-04-19 15:26:41] Average Time: 69.54
[INFO] [2021-04-19 15:26:41] Total Time: 1m34s
[STOP] [2021-04-19 15:26:41] overall_tsv_creation
[INFO] [2021-04-19 15:26:41] Done. Check your files:
[INFO] [2021-04-19 15:26:41] (1 lines) /app/public/data/uuteau/publish_nodes.tsv
[INFO] [2021-04-19 15:26:41] (1 lines) /app/public/data/uuteau/publish_scientific_names.tsv
[INFO] [2021-04-19 15:26:41] (2 lines) /app/public/data/uuteau/publish_traits.tsv
[INFO] [2021-04-19 15:26:41] (3 lines) /app/public/data/uuteau/publish_metadata.tsv
[STOP] [2021-04-19 15:26:41] complete_harvest_instance
[START] [2021-04-19 15:26:41] completed
[STOP] [2021-04-19 15:26:41] completed
[STOP] [2021-04-19 15:26:41] logged process, took 101.28

Latest Process