Stage:
completed
Fetched:
19 Apr 17:11
Validated:
19 Apr 17:11
Deltas Created
19 Apr 17:12
Units Normalized:
19 Apr 17:12
Ancestry Built:
19 Apr 17:12
Nodes Matched:
19 Apr 17:12
Names Parsed:
19 Apr 17:12
New Models Stored:
19 Apr 17:12
Indexed:
19 Apr 17:12
Completed:
19 Apr 17:13
Time to Harvest:
less than a minute
Harvesting Log
(456 lines)
# Logfile created on 2021-02-03 10:51:24 -0500 by logger.rb/v1.4.2
[START] [2021-02-03 10:51:24] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 10:51:24] Creating resource from OpenData
[START] [2021-02-03 10:51:24] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 10:51:24] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 10:51:25] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 10:51:25] Creating resource from OpenData
[INFO] [2021-02-03 10:52:42] ## HARVEST: type = -harvest
[START] [2021-02-03 10:52:43] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 10:52:43] create_harvest_instance
[STOP] [2021-02-03 10:52:44] create_harvest_instance
[START] [2021-02-03 10:52:44] fetch_files
[STOP] [2021-02-03 10:52:44] fetch_files
[START] [2021-02-03 10:52:44] validate_each_file
[STOP] [2021-02-03 10:52:44] validate_each_file
[START] [2021-02-03 10:52:44] convert_to_csv
[CMD] [2021-02-03 10:52:44] /usr/bin/sort /app/public/converted_csv/ldeal_nodes_26602.csv > /app/public/converted_csv/ldeal_nodes_26602.csv_sorted
[CMD] [2021-02-03 10:52:44] /usr/bin/sort /app/public/converted_csv/ldeal_occurrences_26603.csv > /app/public/converted_csv/ldeal_occurrences_26603.csv_sorted
[CMD] [2021-02-03 10:52:44] /usr/bin/sort /app/public/converted_csv/ldeal_measurements_26604.csv > /app/public/converted_csv/ldeal_measurements_26604.csv_sorted
[STOP] [2021-02-03 10:52:44] convert_to_csv
[START] [2021-02-03 10:52:44] calculate_delta
[CMD] [2021-02-03 10:52:44] echo "0a" > /app/public/diff/ldeal_nodes_26602.diff
[CMD] [2021-02-03 10:52:44] tail -n +1 /app/public/converted_csv/ldeal_nodes_26602.csv >> /app/public/diff/ldeal_nodes_26602.diff
[CMD] [2021-02-03 10:52:44] echo "." >> /app/public/diff/ldeal_nodes_26602.diff
[CMD] [2021-02-03 10:52:44] echo "0a" > /app/public/diff/ldeal_occurrences_26603.diff
[CMD] [2021-02-03 10:52:44] tail -n +1 /app/public/converted_csv/ldeal_occurrences_26603.csv >> /app/public/diff/ldeal_occurrences_26603.diff
[CMD] [2021-02-03 10:52:44] echo "." >> /app/public/diff/ldeal_occurrences_26603.diff
[CMD] [2021-02-03 10:52:44] echo "0a" > /app/public/diff/ldeal_measurements_26604.diff
[CMD] [2021-02-03 10:52:44] tail -n +1 /app/public/converted_csv/ldeal_measurements_26604.csv >> /app/public/diff/ldeal_measurements_26604.diff
[CMD] [2021-02-03 10:52:44] echo "." >> /app/public/diff/ldeal_measurements_26604.diff
[STOP] [2021-02-03 10:52:44] calculate_delta
[START] [2021-02-03 10:52:44] parse_diff_and_store
[INFO] [2021-02-03 10:52:44] Loading nodes diff file into memory (true lines)...
[INFO] [2021-02-03 10:52:44] Loading occurrences diff file into memory (true lines)...
[INFO] [2021-02-03 10:52:44] Loading measurements diff file into memory (true lines)...
[INFO] [2021-02-03 10:52:45] Storing 2 ScientificNames
[INFO] [2021-02-03 10:52:45] Processing group of 2 in 1 groups of 1000
[INFO] [2021-02-03 10:52:45] Average Time: 0.0
[INFO] [2021-02-03 10:52:45] Total Time: 1s
[INFO] [2021-02-03 10:52:45] Storing 2 Nodes
[INFO] [2021-02-03 10:52:45] Processing group of 2 in 1 groups of 1000
[INFO] [2021-02-03 10:52:45] Average Time: 0.0
[INFO] [2021-02-03 10:52:45] Total Time: 1s
[INFO] [2021-02-03 10:52:45] Storing 2 Occurrences
[INFO] [2021-02-03 10:52:45] Processing group of 2 in 1 groups of 1000
[INFO] [2021-02-03 10:52:45] Average Time: 0.0
[INFO] [2021-02-03 10:52:45] Total Time: 1s
[INFO] [2021-02-03 10:52:45] Storing 5 Traits
[INFO] [2021-02-03 10:52:45] Processing group of 5 in 1 groups of 1000
[INFO] [2021-02-03 10:52:45] Average Time: 0.0
[INFO] [2021-02-03 10:52:45] Total Time: 1s
[INFO] [2021-02-03 10:52:45] Storing 2 MetaTraits
[INFO] [2021-02-03 10:52:45] Processing group of 2 in 1 groups of 1000
[INFO] [2021-02-03 10:52:45] Average Time: 0.0
[INFO] [2021-02-03 10:52:45] Total Time: 1s
[STOP] [2021-02-03 10:52:45] parse_diff_and_store
[START] [2021-02-03 10:52:45] resolve_keys
[INFO] [2021-02-03 10:52:51] Occurrences to nodes (through scientific_names)...
[INFO] [2021-02-03 10:52:51] traits to occurrences...
[INFO] [2021-02-03 10:52:51] traits to nodes (through occurrences)...
[INFO] [2021-02-03 10:52:51] Traits to sex term...
[INFO] [2021-02-03 10:52:51] Traits to lifestage term...
[INFO] [2021-02-03 10:52:51] MetaTraits to traits...
[INFO] [2021-02-03 10:52:51] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-02-03 10:52:51] Assocs to occurrences...
[INFO] [2021-02-03 10:52:51] Assocs to nodes...
[INFO] [2021-02-03 10:52:51] Assoc to sex term...
[INFO] [2021-02-03 10:52:51] Assoc to lifestage term...
[INFO] [2021-02-03 10:52:51] MetaAssoc to assocs...
[STOP] [2021-02-03 10:52:51] resolve_keys
[START] [2021-02-03 10:52:51] hold_for_later_1
[STOP] [2021-02-03 10:52:51] hold_for_later_1
[START] [2021-02-03 10:52:51] hold_for_later_2
[STOP] [2021-02-03 10:52:51] hold_for_later_2
[START] [2021-02-03 10:52:51] resolve_missing_parents
[STOP] [2021-02-03 10:52:51] resolve_missing_parents
[START] [2021-02-03 10:52:51] rebuild_nodes
[START] [2021-02-03 10:52:51] Flattener#flatten
[START] [2021-02-03 10:52:51] Flattener#study_resource
[START] [2021-02-03 10:52:51] Flattener#build_ancestry
[STOP] [2021-02-03 10:52:51] Flattener#build_ancestry
[INFO] [2021-02-03 10:52:51] 2 ancestry keys
[START] [2021-02-03 10:52:51] build_node_ancestors
[INFO] [2021-02-03 10:52:51] old ancestors deleted.
[STOP] [2021-02-03 10:52:51] build_node_ancestors
[WARN] [2021-02-03 10:52:51] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-02-03 10:52:51] Flattener#flatten
[STOP] [2021-02-03 10:52:51] rebuild_nodes
[START] [2021-02-03 10:52:51] resolve_missing_media_owners
[STOP] [2021-02-03 10:52:51] resolve_missing_media_owners
[START] [2021-02-03 10:52:51] sanitize_media_verbatims
[STOP] [2021-02-03 10:52:51] sanitize_media_verbatims
[START] [2021-02-03 10:52:51] queue_downloads
[STOP] [2021-02-03 10:52:51] queue_downloads
[START] [2021-02-03 10:52:51] parse_names
[WARN] [2021-02-03 10:52:51] I see 2 names which still need to be parsed.
[STOP] [2021-02-03 10:52:52] parse_names
[START] [2021-02-03 10:52:52] denormalize_canonical_names_to_nodes
[STOP] [2021-02-03 10:52:52] denormalize_canonical_names_to_nodes
[START] [2021-02-03 10:52:52] match_nodes
[START] [2021-02-03 10:52:52] map_all_nodes_to_pages
[STOP] [2021-02-03 10:52:52] map_all_nodes_to_pages
[INFO] [2021-02-03 10:52:52] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2021-02-03 10:52:52] update_nodes
[STOP] [2021-02-03 10:52:52] update_nodes
[STOP] [2021-02-03 10:52:52] match_nodes
[START] [2021-02-03 10:52:52] reindex_search
[STOP] [2021-02-03 10:52:52] reindex_search
[START] [2021-02-03 10:52:52] normalize_units
[STOP] [2021-02-03 10:52:52] normalize_units
[START] [2021-02-03 10:52:52] calculate_statistics
[2021-02-03 10:52:52] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-02-03 10:52:52] calculate_statistics
[START] [2021-02-03 10:52:52] complete_harvest_instance
[START] [2021-02-03 10:52:52] overall_tsv_creation
[INFO] [2021-02-03 10:52:52] Processing group of 2 in 1 batches of 10000
[INFO] [2021-02-03 10:53:31] 2 Traits (unfiltered)...
[INFO] [2021-02-03 10:54:08] 2 Traits (filtered)...
[INFO] [2021-02-03 10:54:08] 0 Associations (filtered)...
[INFO] [2021-02-03 10:54:08] 5 metadata added.
[INFO] [2021-02-03 10:54:08] 0 metadata added.
[INFO] [2021-02-03 10:54:39] Average Time: 81.83
[INFO] [2021-02-03 10:54:39] Total Time: 1m48s
[STOP] [2021-02-03 10:54:39] overall_tsv_creation
[INFO] [2021-02-03 10:54:39] Done. Check your files:
[INFO] [2021-02-03 10:54:39] (2 lines) /app/public/data/ldeal/publish_nodes.tsv
[INFO] [2021-02-03 10:54:39] (2 lines) /app/public/data/ldeal/publish_scientific_names.tsv
[INFO] [2021-02-03 10:54:39] (3 lines) /app/public/data/ldeal/publish_traits.tsv
[INFO] [2021-02-03 10:54:39] (6 lines) /app/public/data/ldeal/publish_metadata.tsv
[STOP] [2021-02-03 10:54:39] complete_harvest_instance
[START] [2021-02-03 10:54:39] completed
[STOP] [2021-02-03 10:54:39] completed
[STOP] [2021-02-03 10:54:39] logged process, took 116.9
[INFO] [2021-04-19 16:54:31] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 17:11:58] ## remove_type: ScientificName
[INFO] [2021-04-19 17:11:58] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 17:11:58] [17:11:58.703] Removed 2 Scientificnames
[INFO] [2021-04-19 17:11:58] ## remove_type: Vernacular
[INFO] [2021-04-19 17:11:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:11:58] [17:11:58.704] Removed 0 Vernaculars
[INFO] [2021-04-19 17:11:58] ## remove_type: Article
[INFO] [2021-04-19 17:11:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:11:58] [17:11:58.706] Removed 0 Articles
[INFO] [2021-04-19 17:11:58] ## remove_type: Medium
[INFO] [2021-04-19 17:11:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:11:58] [17:11:58.707] Removed 0 Media
[INFO] [2021-04-19 17:11:58] ## remove_type: Trait
[INFO] [2021-04-19 17:11:58] ++ Calling delete_all on 5 instances...
[INFO] [2021-04-19 17:11:58] [17:11:58.709] Removed 5 Traits
[INFO] [2021-04-19 17:11:58] ## remove_type: MetaTrait
[INFO] [2021-04-19 17:11:58] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 17:11:58] [17:11:58.711] Removed 2 Metatraits
[INFO] [2021-04-19 17:11:58] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 17:11:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:11:58] [17:11:58.712] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 17:11:58] ## remove_type: Assoc
[INFO] [2021-04-19 17:11:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:11:58] [17:11:58.714] Removed 0 Assocs
[INFO] [2021-04-19 17:11:58] ## remove_type: MetaAssoc
[INFO] [2021-04-19 17:11:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:11:58] [17:11:58.715] Removed 0 Metaassocs
[INFO] [2021-04-19 17:11:58] ## remove_type: Identifier
[INFO] [2021-04-19 17:11:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:11:58] [17:11:58.717] Removed 0 Identifiers
[INFO] [2021-04-19 17:11:58] ## remove_type: Reference
[INFO] [2021-04-19 17:11:58] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:11:58] [17:11:58.718] Removed 0 References
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
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[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
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[INFO] [2021-04-19 17:11:58] Starting batch with ID 87728778...
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[INFO] [2021-04-19 17:11:59] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:59] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:59] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:59] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:59] Starting batch with ID 87728778...
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[INFO] [2021-04-19 17:11:59] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:59] Starting batch with ID 87728778...
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[INFO] [2021-04-19 17:11:59] Starting batch with ID 87728778...
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[INFO] [2021-04-19 17:11:59] Starting batch with ID 87728778...
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[INFO] [2021-04-19 17:11:59] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:59] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:59] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:59] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:59] Starting batch with ID 87728778...
[INFO] [2021-04-19 17:11:59] ## remove_type: Node
[INFO] [2021-04-19 17:11:59] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 17:11:59] [17:11:59.533] Removed 2 Nodes
[START] [2021-04-19 17:11:59] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:11:59] Creating resource from OpenData
[START] [2021-04-19 17:11:59] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:11:59] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 17:11:59] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 17:11:59] Creating resource from OpenData
[START] [2021-04-19 17:11:59] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:11:59] create_harvest_instance
[INFO] [2021-04-19 17:11:59] Created harvest instance #3819
[STOP] [2021-04-19 17:11:59] create_harvest_instance
[START] [2021-04-19 17:11:59] fetch_files
[STOP] [2021-04-19 17:11:59] fetch_files
[START] [2021-04-19 17:11:59] validate_each_file
[INFO] [2021-04-19 17:11:59] Looping over 3 formats...
[INFO] [2021-04-19 17:11:59] ...nodes (/app/public/data/ldeal/taxa.txt)
[INFO] [2021-04-19 17:11:59] Valid: /app/public/converted_csv/ldeal_nodes_3819.csv (2 lines)
[INFO] [2021-04-19 17:11:59] ...occurrences (/app/public/data/ldeal/occurrences.txt)
[INFO] [2021-04-19 17:11:59] Valid: /app/public/converted_csv/ldeal_occurrences_3819.csv (2 lines)
[INFO] [2021-04-19 17:11:59] ...measurements (/app/public/data/ldeal/measurementsorfacts.txt)
[INFO] [2021-04-19 17:11:59] Valid: /app/public/converted_csv/ldeal_measurements_3819.csv (5 lines)
[STOP] [2021-04-19 17:11:59] validate_each_file
[START] [2021-04-19 17:11:59] convert_to_csv
[INFO] [2021-04-19 17:11:59] Looping over 3 formats...
[INFO] [2021-04-19 17:11:59] ...nodes (/app/public/data/ldeal/taxa.txt)
[CMD] [2021-04-19 17:11:59] /usr/bin/sort /app/public/converted_csv/ldeal_nodes_3819.csv > /app/public/converted_csv/ldeal_nodes_3819.csv_sorted
[INFO] [2021-04-19 17:11:59] Converted: /app/public/converted_csv/ldeal_nodes_3819.csv (2 lines)
[INFO] [2021-04-19 17:11:59] ...occurrences (/app/public/data/ldeal/occurrences.txt)
[CMD] [2021-04-19 17:11:59] /usr/bin/sort /app/public/converted_csv/ldeal_occurrences_3819.csv > /app/public/converted_csv/ldeal_occurrences_3819.csv_sorted
[INFO] [2021-04-19 17:12:00] Converted: /app/public/converted_csv/ldeal_occurrences_3819.csv (2 lines)
[INFO] [2021-04-19 17:12:00] ...measurements (/app/public/data/ldeal/measurementsorfacts.txt)
[CMD] [2021-04-19 17:12:00] /usr/bin/sort /app/public/converted_csv/ldeal_measurements_3819.csv > /app/public/converted_csv/ldeal_measurements_3819.csv_sorted
[INFO] [2021-04-19 17:12:00] Converted: /app/public/converted_csv/ldeal_measurements_3819.csv (5 lines)
[STOP] [2021-04-19 17:12:00] convert_to_csv
[START] [2021-04-19 17:12:00] calculate_delta
[INFO] [2021-04-19 17:12:00] Looping over 3 formats...
[INFO] [2021-04-19 17:12:00] ...nodes (/app/public/data/ldeal/taxa.txt)
[CMD] [2021-04-19 17:12:00] echo "0a" > /app/public/diff/ldeal_nodes_3819.diff
[CMD] [2021-04-19 17:12:00] tail -n +1 /app/public/converted_csv/ldeal_nodes_3819.csv >> /app/public/diff/ldeal_nodes_3819.diff
[CMD] [2021-04-19 17:12:00] echo "." >> /app/public/diff/ldeal_nodes_3819.diff
[INFO] [2021-04-19 17:12:00] Created diff: /app/public/diff/ldeal_nodes_3819.diff (4 lines)
[INFO] [2021-04-19 17:12:00] ...occurrences (/app/public/data/ldeal/occurrences.txt)
[CMD] [2021-04-19 17:12:00] echo "0a" > /app/public/diff/ldeal_occurrences_3819.diff
[CMD] [2021-04-19 17:12:00] tail -n +1 /app/public/converted_csv/ldeal_occurrences_3819.csv >> /app/public/diff/ldeal_occurrences_3819.diff
[CMD] [2021-04-19 17:12:00] echo "." >> /app/public/diff/ldeal_occurrences_3819.diff
[INFO] [2021-04-19 17:12:00] Created diff: /app/public/diff/ldeal_occurrences_3819.diff (4 lines)
[INFO] [2021-04-19 17:12:00] ...measurements (/app/public/data/ldeal/measurementsorfacts.txt)
[CMD] [2021-04-19 17:12:00] echo "0a" > /app/public/diff/ldeal_measurements_3819.diff
[CMD] [2021-04-19 17:12:00] tail -n +1 /app/public/converted_csv/ldeal_measurements_3819.csv >> /app/public/diff/ldeal_measurements_3819.diff
[CMD] [2021-04-19 17:12:00] echo "." >> /app/public/diff/ldeal_measurements_3819.diff
[INFO] [2021-04-19 17:12:00] Created diff: /app/public/diff/ldeal_measurements_3819.diff (7 lines)
[STOP] [2021-04-19 17:12:00] calculate_delta
[START] [2021-04-19 17:12:00] parse_diff_and_store
[INFO] [2021-04-19 17:12:00] Handling diff: /app/public/diff/ldeal_nodes_3819.diff (4 lines)
[INFO] [2021-04-19 17:12:00] Loading nodes diff file into memory (4 /app/public/diff/ldeal_nodes_3819.diff lines)...
[INFO] [2021-04-19 17:12:00] Handling diff: /app/public/diff/ldeal_occurrences_3819.diff (4 lines)
[INFO] [2021-04-19 17:12:00] Loading occurrences diff file into memory (4 /app/public/diff/ldeal_occurrences_3819.diff lines)...
[INFO] [2021-04-19 17:12:00] Handling diff: /app/public/diff/ldeal_measurements_3819.diff (7 lines)
[INFO] [2021-04-19 17:12:00] Loading measurements diff file into memory (7 /app/public/diff/ldeal_measurements_3819.diff lines)...
[INFO] [2021-04-19 17:12:00] Storing 2 ScientificNames
[INFO] [2021-04-19 17:12:00] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 17:12:00] Average Time: 0.0
[INFO] [2021-04-19 17:12:00] Total Time: 1s
[INFO] [2021-04-19 17:12:00] Storing 2 Nodes
[INFO] [2021-04-19 17:12:00] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 17:12:00] Average Time: 0.0
[INFO] [2021-04-19 17:12:00] Total Time: 1s
[INFO] [2021-04-19 17:12:00] Storing 2 Occurrences
[INFO] [2021-04-19 17:12:00] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 17:12:00] Average Time: 0.0
[INFO] [2021-04-19 17:12:00] Total Time: 1s
[INFO] [2021-04-19 17:12:00] Storing 5 Traits
[INFO] [2021-04-19 17:12:00] Processing group of 5 in 1 groups of 1000
[INFO] [2021-04-19 17:12:00] Average Time: 0.0
[INFO] [2021-04-19 17:12:00] Total Time: 1s
[INFO] [2021-04-19 17:12:00] Storing 2 MetaTraits
[INFO] [2021-04-19 17:12:00] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 17:12:00] Average Time: 0.0
[INFO] [2021-04-19 17:12:00] Total Time: 1s
[STOP] [2021-04-19 17:12:00] parse_diff_and_store
[START] [2021-04-19 17:12:00] resolve_keys
[INFO] [2021-04-19 17:12:06] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 17:12:06] traits to occurrences...
[INFO] [2021-04-19 17:12:06] traits to nodes (through occurrences)...
[INFO] [2021-04-19 17:12:06] Traits to sex term...
[INFO] [2021-04-19 17:12:06] Traits to lifestage term...
[INFO] [2021-04-19 17:12:06] MetaTraits to traits...
[INFO] [2021-04-19 17:12:06] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 17:12:06] Assocs to occurrences...
[INFO] [2021-04-19 17:12:06] Assocs to nodes...
[INFO] [2021-04-19 17:12:06] Assoc to sex term...
[INFO] [2021-04-19 17:12:06] Assoc to lifestage term...
[INFO] [2021-04-19 17:12:06] MetaAssoc to assocs...
[STOP] [2021-04-19 17:12:06] resolve_keys
[START] [2021-04-19 17:12:06] hold_for_later_1
[STOP] [2021-04-19 17:12:06] hold_for_later_1
[START] [2021-04-19 17:12:06] hold_for_later_2
[STOP] [2021-04-19 17:12:06] hold_for_later_2
[START] [2021-04-19 17:12:06] resolve_missing_parents
[STOP] [2021-04-19 17:12:06] resolve_missing_parents
[START] [2021-04-19 17:12:06] rebuild_nodes
[START] [2021-04-19 17:12:06] Flattener#flatten
[START] [2021-04-19 17:12:06] Flattener#study_resource
[START] [2021-04-19 17:12:06] Flattener#build_ancestry
[STOP] [2021-04-19 17:12:06] Flattener#build_ancestry
[INFO] [2021-04-19 17:12:06] 2 ancestry keys
[START] [2021-04-19 17:12:06] build_node_ancestors
[INFO] [2021-04-19 17:12:06] old ancestors deleted.
[STOP] [2021-04-19 17:12:06] build_node_ancestors
[WARN] [2021-04-19 17:12:06] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 17:12:06] Flattener#flatten
[STOP] [2021-04-19 17:12:06] rebuild_nodes
[START] [2021-04-19 17:12:06] resolve_missing_media_owners
[STOP] [2021-04-19 17:12:06] resolve_missing_media_owners
[START] [2021-04-19 17:12:06] sanitize_media_verbatims
[STOP] [2021-04-19 17:12:06] sanitize_media_verbatims
[START] [2021-04-19 17:12:06] queue_downloads
[STOP] [2021-04-19 17:12:06] queue_downloads
[START] [2021-04-19 17:12:06] parse_names
[WARN] [2021-04-19 17:12:06] I see 2 names which still need to be parsed.
[STOP] [2021-04-19 17:12:07] parse_names
[START] [2021-04-19 17:12:07] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 17:12:07] denormalize_canonical_names_to_nodes
[START] [2021-04-19 17:12:07] match_nodes
[START] [2021-04-19 17:12:07] map_all_nodes_to_pages
[STOP] [2021-04-19 17:12:07] map_all_nodes_to_pages
[INFO] [2021-04-19 17:12:07] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2021-04-19 17:12:07] update_nodes
[STOP] [2021-04-19 17:12:07] update_nodes
[STOP] [2021-04-19 17:12:07] match_nodes
[START] [2021-04-19 17:12:07] reindex_search
[STOP] [2021-04-19 17:12:07] reindex_search
[START] [2021-04-19 17:12:07] normalize_units
[STOP] [2021-04-19 17:12:07] normalize_units
[START] [2021-04-19 17:12:07] calculate_statistics
[2021-04-19 17:12:07] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 17:12:07] calculate_statistics
[START] [2021-04-19 17:12:07] complete_harvest_instance
[START] [2021-04-19 17:12:07] overall_tsv_creation
[INFO] [2021-04-19 17:12:07] Processing group of 2 in 1 batches of 10000
[INFO] [2021-04-19 17:12:43] 2 Traits (unfiltered)...
[INFO] [2021-04-19 17:13:17] 2 Traits (filtered)...
[INFO] [2021-04-19 17:13:17] 0 Associations (filtered)...
[INFO] [2021-04-19 17:13:17] 3 metadata added.
[INFO] [2021-04-19 17:13:17] 0 metadata added.
[INFO] [2021-04-19 17:13:44] Average Time: 73.53
[INFO] [2021-04-19 17:13:44] Total Time: 1m38s
[STOP] [2021-04-19 17:13:44] overall_tsv_creation
[INFO] [2021-04-19 17:13:44] Done. Check your files:
[INFO] [2021-04-19 17:13:44] (2 lines) /app/public/data/ldeal/publish_nodes.tsv
[INFO] [2021-04-19 17:13:44] (2 lines) /app/public/data/ldeal/publish_scientific_names.tsv
[INFO] [2021-04-19 17:13:44] (3 lines) /app/public/data/ldeal/publish_traits.tsv
[INFO] [2021-04-19 17:13:44] (4 lines) /app/public/data/ldeal/publish_metadata.tsv
[STOP] [2021-04-19 17:13:44] complete_harvest_instance
[START] [2021-04-19 17:13:44] completed
[STOP] [2021-04-19 17:13:44] completed
[STOP] [2021-04-19 17:13:44] logged process, took 105.02
Latest Process