Harvest for Owens and Lewis 2018 Created 19 Apr 17:15

Stage: completed
Fetched: 19 Apr 17:15
Validated: 19 Apr 17:15
Deltas Created 19 Apr 17:15
Units Normalized: 19 Apr 17:15
Ancestry Built: 19 Apr 17:15
Nodes Matched: 19 Apr 17:15
Names Parsed: 19 Apr 17:15
New Models Stored: 19 Apr 17:15
Indexed: 19 Apr 17:15
Completed: 19 Apr 17:17
Time to Harvest: less than a minute
Harvesting Log

(480 lines)
# Logfile created on 2021-02-03 11:00:29 -0500 by logger.rb/v1.4.2
[START] [2021-02-03 11:00:29] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 11:00:29] Creating resource from OpenData
[START] [2021-02-03 11:00:30] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 11:00:30] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:00:30] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:00:30] Creating resource from OpenData
[INFO] [2021-02-03 11:04:56] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-02-03 11:04:57] ## remove_type: ScientificName
[INFO] [2021-02-03 11:04:57] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:04:57] [11:04:57.450] Removed 0 Scientificnames
[INFO] [2021-02-03 11:04:57] ## remove_type: Vernacular
[INFO] [2021-02-03 11:04:57] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:04:57] [11:04:57.453] Removed 0 Vernaculars
[INFO] [2021-02-03 11:04:57] ## remove_type: Article
[INFO] [2021-02-03 11:04:57] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:04:57] [11:04:57.456] Removed 0 Articles
[INFO] [2021-02-03 11:04:57] ## remove_type: Medium
[INFO] [2021-02-03 11:04:57] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:04:57] [11:04:57.460] Removed 0 Media
[INFO] [2021-02-03 11:04:57] ## remove_type: Trait
[INFO] [2021-02-03 11:04:57] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:04:57] [11:04:57.463] Removed 0 Traits
[INFO] [2021-02-03 11:04:57] ## remove_type: MetaTrait
[INFO] [2021-02-03 11:04:57] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:04:57] [11:04:57.466] Removed 0 Metatraits
[INFO] [2021-02-03 11:04:57] ## remove_type: OccurrenceMetadatum
[INFO] [2021-02-03 11:04:57] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:04:57] [11:04:57.469] Removed 0 Occurrencemetadata
[INFO] [2021-02-03 11:04:57] ## remove_type: Assoc
[INFO] [2021-02-03 11:04:57] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:04:57] [11:04:57.472] Removed 0 Assocs
[INFO] [2021-02-03 11:04:57] ## remove_type: MetaAssoc
[INFO] [2021-02-03 11:04:57] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:04:57] [11:04:57.475] Removed 0 Metaassocs
[INFO] [2021-02-03 11:04:57] ## remove_type: Identifier
[INFO] [2021-02-03 11:04:57] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:04:57] [11:04:57.478] Removed 0 Identifiers
[INFO] [2021-02-03 11:04:57] ## remove_type: Reference
[INFO] [2021-02-03 11:04:57] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:04:57] [11:04:57.480] Removed 0 References
[INFO] [2021-02-03 11:04:57] ## remove_type: Node
[INFO] [2021-02-03 11:04:57] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:04:57] [11:04:57.502] Removed 0 Nodes
[START] [2021-02-03 11:04:57] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 11:04:57] Creating resource from OpenData
[START] [2021-02-03 11:04:57] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 11:04:57] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:04:57] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:04:57] Creating resource from OpenData
[START] [2021-02-03 11:04:57] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977

[START] [2021-02-03 11:04:57] create_harvest_instance
[STOP] [2021-02-03 11:04:59] create_harvest_instance
[START] [2021-02-03 11:04:59] fetch_files
[STOP] [2021-02-03 11:04:59] fetch_files
[START] [2021-02-03 11:04:59] validate_each_file
[STOP] [2021-02-03 11:04:59] validate_each_file
[START] [2021-02-03 11:04:59] convert_to_csv
[CMD] [2021-02-03 11:04:59] /usr/bin/sort /app/public/converted_csv/owens_lewis_owen_nodes_26632.csv > /app/public/converted_csv/owens_lewis_owen_nodes_26632.csv_sorted
[CMD] [2021-02-03 11:04:59] /usr/bin/sort /app/public/converted_csv/owens_lewis_owen_occurrences_26633.csv > /app/public/converted_csv/owens_lewis_owen_occurrences_26633.csv_sorted
[CMD] [2021-02-03 11:04:59] /usr/bin/sort /app/public/converted_csv/owens_lewis_owen_measurements_26634.csv > /app/public/converted_csv/owens_lewis_owen_measurements_26634.csv_sorted
[STOP] [2021-02-03 11:04:59] convert_to_csv
[START] [2021-02-03 11:04:59] calculate_delta
[CMD] [2021-02-03 11:04:59] echo "0a" > /app/public/diff/owens_lewis_owen_nodes_26632.diff
[CMD] [2021-02-03 11:04:59] tail -n +1 /app/public/converted_csv/owens_lewis_owen_nodes_26632.csv >> /app/public/diff/owens_lewis_owen_nodes_26632.diff
[CMD] [2021-02-03 11:04:59] echo "." >> /app/public/diff/owens_lewis_owen_nodes_26632.diff
[CMD] [2021-02-03 11:04:59] echo "0a" > /app/public/diff/owens_lewis_owen_occurrences_26633.diff
[CMD] [2021-02-03 11:04:59] tail -n +1 /app/public/converted_csv/owens_lewis_owen_occurrences_26633.csv >> /app/public/diff/owens_lewis_owen_occurrences_26633.diff
[CMD] [2021-02-03 11:04:59] echo "." >> /app/public/diff/owens_lewis_owen_occurrences_26633.diff
[CMD] [2021-02-03 11:04:59] echo "0a" > /app/public/diff/owens_lewis_owen_measurements_26634.diff
[CMD] [2021-02-03 11:04:59] tail -n +1 /app/public/converted_csv/owens_lewis_owen_measurements_26634.csv >> /app/public/diff/owens_lewis_owen_measurements_26634.diff
[CMD] [2021-02-03 11:04:59] echo "." >> /app/public/diff/owens_lewis_owen_measurements_26634.diff
[STOP] [2021-02-03 11:04:59] calculate_delta
[START] [2021-02-03 11:04:59] parse_diff_and_store
[INFO] [2021-02-03 11:04:59] Loading nodes diff file into memory (true lines)...
[INFO] [2021-02-03 11:04:59] Loading occurrences diff file into memory (true lines)...
[INFO] [2021-02-03 11:05:00] Loading measurements diff file into memory (true lines)...
[INFO] [2021-02-03 11:05:00] Storing 3 ScientificNames
[INFO] [2021-02-03 11:05:00] Processing group of 3 in 1 groups of 1000
[INFO] [2021-02-03 11:05:00] Average Time: 0.0
[INFO] [2021-02-03 11:05:00] Total Time: 1s
[INFO] [2021-02-03 11:05:00] Storing 3 Nodes
[INFO] [2021-02-03 11:05:00] Processing group of 3 in 1 groups of 1000
[INFO] [2021-02-03 11:05:00] Average Time: 0.0
[INFO] [2021-02-03 11:05:00] Total Time: 1s
[INFO] [2021-02-03 11:05:00] Storing 3 Occurrences
[INFO] [2021-02-03 11:05:00] Processing group of 3 in 1 groups of 1000
[INFO] [2021-02-03 11:05:00] Average Time: 0.0
[INFO] [2021-02-03 11:05:00] Total Time: 1s
[INFO] [2021-02-03 11:05:00] Storing 3 OccurrenceMetadata
[INFO] [2021-02-03 11:05:00] Processing group of 3 in 1 groups of 1000
[INFO] [2021-02-03 11:05:00] Average Time: 0.0
[INFO] [2021-02-03 11:05:00] Total Time: 1s
[INFO] [2021-02-03 11:05:00] Storing 15 Traits
[INFO] [2021-02-03 11:05:00] Processing group of 15 in 1 groups of 1000
[INFO] [2021-02-03 11:05:00] Average Time: 0.01
[INFO] [2021-02-03 11:05:00] Total Time: 1s
[INFO] [2021-02-03 11:05:00] Storing 3 MetaTraits
[INFO] [2021-02-03 11:05:00] Processing group of 3 in 1 groups of 1000
[INFO] [2021-02-03 11:05:00] Average Time: 0.0
[INFO] [2021-02-03 11:05:00] Total Time: 1s
[STOP] [2021-02-03 11:05:00] parse_diff_and_store
[START] [2021-02-03 11:05:00] resolve_keys
[INFO] [2021-02-03 11:05:06] Occurrences to nodes (through scientific_names)...
[INFO] [2021-02-03 11:05:06] traits to occurrences...
[INFO] [2021-02-03 11:05:06] traits to nodes (through occurrences)...
[INFO] [2021-02-03 11:05:06] Traits to sex term...
[INFO] [2021-02-03 11:05:06] Traits to lifestage term...
[INFO] [2021-02-03 11:05:06] MetaTraits to traits...
[INFO] [2021-02-03 11:05:06] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-02-03 11:05:06] Assocs to occurrences...
[INFO] [2021-02-03 11:05:06] Assocs to nodes...
[INFO] [2021-02-03 11:05:06] Assoc to sex term...
[INFO] [2021-02-03 11:05:06] Assoc to lifestage term...
[INFO] [2021-02-03 11:05:06] MetaAssoc to assocs...
[STOP] [2021-02-03 11:05:06] resolve_keys
[START] [2021-02-03 11:05:06] hold_for_later_1
[STOP] [2021-02-03 11:05:06] hold_for_later_1
[START] [2021-02-03 11:05:06] hold_for_later_2
[STOP] [2021-02-03 11:05:06] hold_for_later_2
[START] [2021-02-03 11:05:06] resolve_missing_parents
[STOP] [2021-02-03 11:05:06] resolve_missing_parents
[START] [2021-02-03 11:05:06] rebuild_nodes
[START] [2021-02-03 11:05:06] Flattener#flatten
[START] [2021-02-03 11:05:06] Flattener#study_resource
[START] [2021-02-03 11:05:06] Flattener#build_ancestry
[STOP] [2021-02-03 11:05:06] Flattener#build_ancestry
[INFO] [2021-02-03 11:05:06] 3 ancestry keys
[START] [2021-02-03 11:05:06] build_node_ancestors
[INFO] [2021-02-03 11:05:06] old ancestors deleted.
[STOP] [2021-02-03 11:05:06] build_node_ancestors
[WARN] [2021-02-03 11:05:06] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-02-03 11:05:06] Flattener#flatten
[STOP] [2021-02-03 11:05:06] rebuild_nodes
[START] [2021-02-03 11:05:06] resolve_missing_media_owners
[STOP] [2021-02-03 11:05:06] resolve_missing_media_owners
[START] [2021-02-03 11:05:06] sanitize_media_verbatims
[STOP] [2021-02-03 11:05:06] sanitize_media_verbatims
[START] [2021-02-03 11:05:06] queue_downloads
[STOP] [2021-02-03 11:05:06] queue_downloads
[START] [2021-02-03 11:05:06] parse_names
[WARN] [2021-02-03 11:05:06] I see 3 names which still need to be parsed.
[STOP] [2021-02-03 11:05:07] parse_names
[START] [2021-02-03 11:05:07] denormalize_canonical_names_to_nodes
[STOP] [2021-02-03 11:05:07] denormalize_canonical_names_to_nodes
[START] [2021-02-03 11:05:07] match_nodes
[START] [2021-02-03 11:05:07] map_all_nodes_to_pages
[STOP] [2021-02-03 11:05:07] map_all_nodes_to_pages
[INFO] [2021-02-03 11:05:07] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2021-02-03 11:05:07] update_nodes
[STOP] [2021-02-03 11:05:07] update_nodes
[STOP] [2021-02-03 11:05:07] match_nodes
[START] [2021-02-03 11:05:07] reindex_search
[STOP] [2021-02-03 11:05:07] reindex_search
[START] [2021-02-03 11:05:07] normalize_units
[STOP] [2021-02-03 11:05:07] normalize_units
[START] [2021-02-03 11:05:07] calculate_statistics
[2021-02-03 11:05:07] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-02-03 11:05:07] calculate_statistics
[START] [2021-02-03 11:05:07] complete_harvest_instance
[START] [2021-02-03 11:05:07] overall_tsv_creation
[INFO] [2021-02-03 11:05:07] Processing group of 3 in 1 batches of 10000
[INFO] [2021-02-03 11:05:46] 3 Traits (unfiltered)...
[INFO] [2021-02-03 11:06:23] 3 Traits (filtered)...
[INFO] [2021-02-03 11:06:23] 0 Associations (filtered)...
[INFO] [2021-02-03 11:06:23] 15 metadata added.
[INFO] [2021-02-03 11:06:23] 0 metadata added.
[INFO] [2021-02-03 11:06:56] Average Time: 82.82
[INFO] [2021-02-03 11:06:56] Total Time: 1m49s
[STOP] [2021-02-03 11:06:56] overall_tsv_creation
[INFO] [2021-02-03 11:06:56] Done. Check your files:
[INFO] [2021-02-03 11:06:56] (3 lines) /app/public/data/owens_lewis_owen/publish_nodes.tsv
[INFO] [2021-02-03 11:06:56] (3 lines) /app/public/data/owens_lewis_owen/publish_scientific_names.tsv
[INFO] [2021-02-03 11:06:56] (4 lines) /app/public/data/owens_lewis_owen/publish_traits.tsv
[INFO] [2021-02-03 11:06:56] (16 lines) /app/public/data/owens_lewis_owen/publish_metadata.tsv
[STOP] [2021-02-03 11:06:56] complete_harvest_instance
[START] [2021-02-03 11:06:56] completed
[STOP] [2021-02-03 11:06:56] completed
[STOP] [2021-02-03 11:06:56] logged process, took 118.47
[INFO] [2021-04-19 16:54:37] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 17:15:29] ## remove_type: ScientificName
[INFO] [2021-04-19 17:15:29] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 17:15:29] [17:15:29.150] Removed 3 Scientificnames
[INFO] [2021-04-19 17:15:29] ## remove_type: Vernacular
[INFO] [2021-04-19 17:15:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:15:29] [17:15:29.152] Removed 0 Vernaculars
[INFO] [2021-04-19 17:15:29] ## remove_type: Article
[INFO] [2021-04-19 17:15:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:15:29] [17:15:29.153] Removed 0 Articles
[INFO] [2021-04-19 17:15:29] ## remove_type: Medium
[INFO] [2021-04-19 17:15:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:15:29] [17:15:29.155] Removed 0 Media
[INFO] [2021-04-19 17:15:29] ## remove_type: Trait
[INFO] [2021-04-19 17:15:29] ++ Calling delete_all on 15 instances...
[INFO] [2021-04-19 17:15:29] [17:15:29.157] Removed 15 Traits
[INFO] [2021-04-19 17:15:29] ## remove_type: MetaTrait
[INFO] [2021-04-19 17:15:29] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 17:15:29] [17:15:29.159] Removed 3 Metatraits
[INFO] [2021-04-19 17:15:29] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 17:15:29] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 17:15:29] [17:15:29.161] Removed 3 Occurrencemetadata
[INFO] [2021-04-19 17:15:29] ## remove_type: Assoc
[INFO] [2021-04-19 17:15:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:15:29] [17:15:29.162] Removed 0 Assocs
[INFO] [2021-04-19 17:15:29] ## remove_type: MetaAssoc
[INFO] [2021-04-19 17:15:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:15:29] [17:15:29.163] Removed 0 Metaassocs
[INFO] [2021-04-19 17:15:29] ## remove_type: Identifier
[INFO] [2021-04-19 17:15:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:15:29] [17:15:29.165] Removed 0 Identifiers
[INFO] [2021-04-19 17:15:29] ## remove_type: Reference
[INFO] [2021-04-19 17:15:29] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:15:29] [17:15:29.166] Removed 0 References
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] Starting batch with ID 87728807...
[INFO] [2021-04-19 17:15:29] ## remove_type: Node
[INFO] [2021-04-19 17:15:29] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 17:15:29] [17:15:29.809] Removed 3 Nodes
[START] [2021-04-19 17:15:29] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:15:29] Creating resource from OpenData
[START] [2021-04-19 17:15:30] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:15:30] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 17:15:30] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 17:15:30] Creating resource from OpenData
[START] [2021-04-19 17:15:30] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:15:30] create_harvest_instance
[INFO] [2021-04-19 17:15:30] Created harvest instance #3821
[STOP] [2021-04-19 17:15:30] create_harvest_instance
[START] [2021-04-19 17:15:30] fetch_files
[STOP] [2021-04-19 17:15:30] fetch_files
[START] [2021-04-19 17:15:30] validate_each_file
[INFO] [2021-04-19 17:15:30] Looping over 3 formats...
[INFO] [2021-04-19 17:15:30] ...nodes (/app/public/data/owens_lewis_owen/taxa.txt)
[INFO] [2021-04-19 17:15:30] Valid: /app/public/converted_csv/owens_lewis_owen_nodes_3821.csv (3 lines)
[INFO] [2021-04-19 17:15:30] ...occurrences (/app/public/data/owens_lewis_owen/occurrences.txt)
[INFO] [2021-04-19 17:15:30] Valid: /app/public/converted_csv/owens_lewis_owen_occurrences_3821.csv (3 lines)
[INFO] [2021-04-19 17:15:30] ...measurements (/app/public/data/owens_lewis_owen/measurementsorfacts.txt)
[INFO] [2021-04-19 17:15:30] Valid: /app/public/converted_csv/owens_lewis_owen_measurements_3821.csv (15 lines)
[STOP] [2021-04-19 17:15:30] validate_each_file
[START] [2021-04-19 17:15:30] convert_to_csv
[INFO] [2021-04-19 17:15:30] Looping over 3 formats...
[INFO] [2021-04-19 17:15:30] ...nodes (/app/public/data/owens_lewis_owen/taxa.txt)
[CMD] [2021-04-19 17:15:30] /usr/bin/sort /app/public/converted_csv/owens_lewis_owen_nodes_3821.csv > /app/public/converted_csv/owens_lewis_owen_nodes_3821.csv_sorted
[INFO] [2021-04-19 17:15:30] Converted: /app/public/converted_csv/owens_lewis_owen_nodes_3821.csv (3 lines)
[INFO] [2021-04-19 17:15:30] ...occurrences (/app/public/data/owens_lewis_owen/occurrences.txt)
[CMD] [2021-04-19 17:15:30] /usr/bin/sort /app/public/converted_csv/owens_lewis_owen_occurrences_3821.csv > /app/public/converted_csv/owens_lewis_owen_occurrences_3821.csv_sorted
[INFO] [2021-04-19 17:15:30] Converted: /app/public/converted_csv/owens_lewis_owen_occurrences_3821.csv (3 lines)
[INFO] [2021-04-19 17:15:30] ...measurements (/app/public/data/owens_lewis_owen/measurementsorfacts.txt)
[CMD] [2021-04-19 17:15:30] /usr/bin/sort /app/public/converted_csv/owens_lewis_owen_measurements_3821.csv > /app/public/converted_csv/owens_lewis_owen_measurements_3821.csv_sorted
[INFO] [2021-04-19 17:15:30] Converted: /app/public/converted_csv/owens_lewis_owen_measurements_3821.csv (15 lines)
[STOP] [2021-04-19 17:15:30] convert_to_csv
[START] [2021-04-19 17:15:30] calculate_delta
[INFO] [2021-04-19 17:15:30] Looping over 3 formats...
[INFO] [2021-04-19 17:15:30] ...nodes (/app/public/data/owens_lewis_owen/taxa.txt)
[CMD] [2021-04-19 17:15:30] echo "0a" > /app/public/diff/owens_lewis_owen_nodes_3821.diff
[CMD] [2021-04-19 17:15:30] tail -n +1 /app/public/converted_csv/owens_lewis_owen_nodes_3821.csv >> /app/public/diff/owens_lewis_owen_nodes_3821.diff
[CMD] [2021-04-19 17:15:30] echo "." >> /app/public/diff/owens_lewis_owen_nodes_3821.diff
[INFO] [2021-04-19 17:15:30] Created diff: /app/public/diff/owens_lewis_owen_nodes_3821.diff (5 lines)
[INFO] [2021-04-19 17:15:30] ...occurrences (/app/public/data/owens_lewis_owen/occurrences.txt)
[CMD] [2021-04-19 17:15:30] echo "0a" > /app/public/diff/owens_lewis_owen_occurrences_3821.diff
[CMD] [2021-04-19 17:15:30] tail -n +1 /app/public/converted_csv/owens_lewis_owen_occurrences_3821.csv >> /app/public/diff/owens_lewis_owen_occurrences_3821.diff
[CMD] [2021-04-19 17:15:30] echo "." >> /app/public/diff/owens_lewis_owen_occurrences_3821.diff
[INFO] [2021-04-19 17:15:30] Created diff: /app/public/diff/owens_lewis_owen_occurrences_3821.diff (5 lines)
[INFO] [2021-04-19 17:15:30] ...measurements (/app/public/data/owens_lewis_owen/measurementsorfacts.txt)
[CMD] [2021-04-19 17:15:30] echo "0a" > /app/public/diff/owens_lewis_owen_measurements_3821.diff
[CMD] [2021-04-19 17:15:30] tail -n +1 /app/public/converted_csv/owens_lewis_owen_measurements_3821.csv >> /app/public/diff/owens_lewis_owen_measurements_3821.diff
[CMD] [2021-04-19 17:15:30] echo "." >> /app/public/diff/owens_lewis_owen_measurements_3821.diff
[INFO] [2021-04-19 17:15:30] Created diff: /app/public/diff/owens_lewis_owen_measurements_3821.diff (17 lines)
[STOP] [2021-04-19 17:15:30] calculate_delta
[START] [2021-04-19 17:15:30] parse_diff_and_store
[INFO] [2021-04-19 17:15:30] Handling diff: /app/public/diff/owens_lewis_owen_nodes_3821.diff (5 lines)
[INFO] [2021-04-19 17:15:30] Loading nodes diff file into memory (5 /app/public/diff/owens_lewis_owen_nodes_3821.diff lines)...
[INFO] [2021-04-19 17:15:30] Handling diff: /app/public/diff/owens_lewis_owen_occurrences_3821.diff (5 lines)
[INFO] [2021-04-19 17:15:30] Loading occurrences diff file into memory (5 /app/public/diff/owens_lewis_owen_occurrences_3821.diff lines)...
[INFO] [2021-04-19 17:15:30] Handling diff: /app/public/diff/owens_lewis_owen_measurements_3821.diff (17 lines)
[INFO] [2021-04-19 17:15:30] Loading measurements diff file into memory (17 /app/public/diff/owens_lewis_owen_measurements_3821.diff lines)...
[INFO] [2021-04-19 17:15:30] Storing 3 ScientificNames
[INFO] [2021-04-19 17:15:30] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 17:15:30] Average Time: 0.0
[INFO] [2021-04-19 17:15:30] Total Time: 1s
[INFO] [2021-04-19 17:15:30] Storing 3 Nodes
[INFO] [2021-04-19 17:15:30] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 17:15:30] Average Time: 0.0
[INFO] [2021-04-19 17:15:30] Total Time: 1s
[INFO] [2021-04-19 17:15:30] Storing 3 Occurrences
[INFO] [2021-04-19 17:15:30] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 17:15:30] Average Time: 0.0
[INFO] [2021-04-19 17:15:30] Total Time: 1s
[INFO] [2021-04-19 17:15:30] Storing 3 OccurrenceMetadata
[INFO] [2021-04-19 17:15:30] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 17:15:30] Average Time: 0.0
[INFO] [2021-04-19 17:15:30] Total Time: 1s
[INFO] [2021-04-19 17:15:30] Storing 15 Traits
[INFO] [2021-04-19 17:15:30] Processing group of 15 in 1 groups of 1000
[INFO] [2021-04-19 17:15:30] Average Time: 0.01
[INFO] [2021-04-19 17:15:30] Total Time: 1s
[INFO] [2021-04-19 17:15:30] Storing 3 MetaTraits
[INFO] [2021-04-19 17:15:30] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 17:15:30] Average Time: 0.0
[INFO] [2021-04-19 17:15:30] Total Time: 1s
[STOP] [2021-04-19 17:15:30] parse_diff_and_store
[START] [2021-04-19 17:15:30] resolve_keys
[INFO] [2021-04-19 17:15:36] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 17:15:36] traits to occurrences...
[INFO] [2021-04-19 17:15:36] traits to nodes (through occurrences)...
[INFO] [2021-04-19 17:15:36] Traits to sex term...
[INFO] [2021-04-19 17:15:36] Traits to lifestage term...
[INFO] [2021-04-19 17:15:36] MetaTraits to traits...
[INFO] [2021-04-19 17:15:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 17:15:36] Assocs to occurrences...
[INFO] [2021-04-19 17:15:36] Assocs to nodes...
[INFO] [2021-04-19 17:15:36] Assoc to sex term...
[INFO] [2021-04-19 17:15:36] Assoc to lifestage term...
[INFO] [2021-04-19 17:15:36] MetaAssoc to assocs...
[STOP] [2021-04-19 17:15:36] resolve_keys
[START] [2021-04-19 17:15:36] hold_for_later_1
[STOP] [2021-04-19 17:15:36] hold_for_later_1
[START] [2021-04-19 17:15:36] hold_for_later_2
[STOP] [2021-04-19 17:15:36] hold_for_later_2
[START] [2021-04-19 17:15:36] resolve_missing_parents
[STOP] [2021-04-19 17:15:36] resolve_missing_parents
[START] [2021-04-19 17:15:36] rebuild_nodes
[START] [2021-04-19 17:15:36] Flattener#flatten
[START] [2021-04-19 17:15:36] Flattener#study_resource
[START] [2021-04-19 17:15:36] Flattener#build_ancestry
[STOP] [2021-04-19 17:15:36] Flattener#build_ancestry
[INFO] [2021-04-19 17:15:36] 3 ancestry keys
[START] [2021-04-19 17:15:36] build_node_ancestors
[INFO] [2021-04-19 17:15:36] old ancestors deleted.
[STOP] [2021-04-19 17:15:36] build_node_ancestors
[WARN] [2021-04-19 17:15:36] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 17:15:36] Flattener#flatten
[STOP] [2021-04-19 17:15:36] rebuild_nodes
[START] [2021-04-19 17:15:36] resolve_missing_media_owners
[STOP] [2021-04-19 17:15:36] resolve_missing_media_owners
[START] [2021-04-19 17:15:36] sanitize_media_verbatims
[STOP] [2021-04-19 17:15:36] sanitize_media_verbatims
[START] [2021-04-19 17:15:36] queue_downloads
[STOP] [2021-04-19 17:15:36] queue_downloads
[START] [2021-04-19 17:15:36] parse_names
[WARN] [2021-04-19 17:15:36] I see 3 names which still need to be parsed.
[STOP] [2021-04-19 17:15:37] parse_names
[START] [2021-04-19 17:15:37] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 17:15:37] denormalize_canonical_names_to_nodes
[START] [2021-04-19 17:15:37] match_nodes
[START] [2021-04-19 17:15:37] map_all_nodes_to_pages
[STOP] [2021-04-19 17:15:37] map_all_nodes_to_pages
[INFO] [2021-04-19 17:15:37] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2021-04-19 17:15:37] update_nodes
[STOP] [2021-04-19 17:15:37] update_nodes
[STOP] [2021-04-19 17:15:37] match_nodes
[START] [2021-04-19 17:15:37] reindex_search
[STOP] [2021-04-19 17:15:37] reindex_search
[START] [2021-04-19 17:15:37] normalize_units
[STOP] [2021-04-19 17:15:37] normalize_units
[START] [2021-04-19 17:15:37] calculate_statistics
[2021-04-19 17:15:37] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 17:15:37] calculate_statistics
[START] [2021-04-19 17:15:37] complete_harvest_instance
[START] [2021-04-19 17:15:37] overall_tsv_creation
[INFO] [2021-04-19 17:15:37] Processing group of 3 in 1 batches of 10000
[INFO] [2021-04-19 17:16:13] 3 Traits (unfiltered)...
[INFO] [2021-04-19 17:16:47] 3 Traits (filtered)...
[INFO] [2021-04-19 17:16:47] 0 Associations (filtered)...
[INFO] [2021-04-19 17:16:47] 12 metadata added.
[INFO] [2021-04-19 17:16:47] 0 metadata added.
[INFO] [2021-04-19 17:17:14] Average Time: 72.31
[INFO] [2021-04-19 17:17:14] Total Time: 1m37s
[STOP] [2021-04-19 17:17:14] overall_tsv_creation
[INFO] [2021-04-19 17:17:14] Done. Check your files:
[INFO] [2021-04-19 17:17:14] (3 lines) /app/public/data/owens_lewis_owen/publish_nodes.tsv
[INFO] [2021-04-19 17:17:14] (3 lines) /app/public/data/owens_lewis_owen/publish_scientific_names.tsv
[INFO] [2021-04-19 17:17:14] (4 lines) /app/public/data/owens_lewis_owen/publish_traits.tsv
[INFO] [2021-04-19 17:17:14] (13 lines) /app/public/data/owens_lewis_owen/publish_metadata.tsv
[STOP] [2021-04-19 17:17:14] complete_harvest_instance
[START] [2021-04-19 17:17:14] completed
[STOP] [2021-04-19 17:17:14] completed
[STOP] [2021-04-19 17:17:14] logged process, took 103.89
Latest Process

19 Apr 17:15 EXITED currently processing 0