Stage:
completed
Fetched:
19 Apr 16:56
Validated:
19 Apr 16:56
Deltas Created
19 Apr 16:56
Units Normalized:
19 Apr 16:56
Ancestry Built:
19 Apr 16:56
Nodes Matched:
19 Apr 16:56
Names Parsed:
19 Apr 16:56
New Models Stored:
19 Apr 16:56
Indexed:
19 Apr 16:56
Completed:
19 Apr 16:58
Time to Harvest:
less than a minute
Harvesting Log
(452 lines)
# Logfile created on 2020-12-08 15:01:00 -0500 by logger.rb/v1.4.2
[START] [2020-12-08 15:01:00] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-08 15:01:00] Creating resource from OpenData
[START] [2020-12-08 15:01:01] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-08 15:01:01] Parse meta.xml file and create formats with fields
[STOP] [2020-12-08 15:01:01] Parse meta.xml file and create formats with fields
[STOP] [2020-12-08 15:01:01] Creating resource from OpenData
[INFO] [2020-12-08 15:01:23] ## HARVEST: type = -harvest
[START] [2020-12-08 15:01:28] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-08 15:01:28] create_harvest_instance
[STOP] [2020-12-08 15:01:29] create_harvest_instance
[START] [2020-12-08 15:01:29] fetch_files
[STOP] [2020-12-08 15:01:29] fetch_files
[START] [2020-12-08 15:01:29] validate_each_file
[STOP] [2020-12-08 15:01:29] validate_each_file
[START] [2020-12-08 15:01:29] convert_to_csv
[CMD] [2020-12-08 15:01:29] /usr/bin/sort /app/public/converted_csv/rintoul_et_al_ri_nodes_25291.csv > /app/public/converted_csv/rintoul_et_al_ri_nodes_25291.csv_sorted
[CMD] [2020-12-08 15:01:29] /usr/bin/sort /app/public/converted_csv/rintoul_et_al_ri_occurrences_25292.csv > /app/public/converted_csv/rintoul_et_al_ri_occurrences_25292.csv_sorted
[CMD] [2020-12-08 15:01:29] /usr/bin/sort /app/public/converted_csv/rintoul_et_al_ri_measurements_25293.csv > /app/public/converted_csv/rintoul_et_al_ri_measurements_25293.csv_sorted
[STOP] [2020-12-08 15:01:29] convert_to_csv
[START] [2020-12-08 15:01:29] calculate_delta
[CMD] [2020-12-08 15:01:29] echo "0a" > /app/public/diff/rintoul_et_al_ri_nodes_25291.diff
[CMD] [2020-12-08 15:01:29] tail -n +1 /app/public/converted_csv/rintoul_et_al_ri_nodes_25291.csv >> /app/public/diff/rintoul_et_al_ri_nodes_25291.diff
[CMD] [2020-12-08 15:01:29] echo "." >> /app/public/diff/rintoul_et_al_ri_nodes_25291.diff
[CMD] [2020-12-08 15:01:29] echo "0a" > /app/public/diff/rintoul_et_al_ri_occurrences_25292.diff
[CMD] [2020-12-08 15:01:29] tail -n +1 /app/public/converted_csv/rintoul_et_al_ri_occurrences_25292.csv >> /app/public/diff/rintoul_et_al_ri_occurrences_25292.diff
[CMD] [2020-12-08 15:01:29] echo "." >> /app/public/diff/rintoul_et_al_ri_occurrences_25292.diff
[CMD] [2020-12-08 15:01:29] echo "0a" > /app/public/diff/rintoul_et_al_ri_measurements_25293.diff
[CMD] [2020-12-08 15:01:29] tail -n +1 /app/public/converted_csv/rintoul_et_al_ri_measurements_25293.csv >> /app/public/diff/rintoul_et_al_ri_measurements_25293.diff
[CMD] [2020-12-08 15:01:29] echo "." >> /app/public/diff/rintoul_et_al_ri_measurements_25293.diff
[STOP] [2020-12-08 15:01:29] calculate_delta
[START] [2020-12-08 15:01:29] parse_diff_and_store
[INFO] [2020-12-08 15:01:29] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-08 15:01:30] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-08 15:01:30] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-08 15:01:30] Storing 3 ScientificNames
[INFO] [2020-12-08 15:01:30] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-08 15:01:30] Average Time: 0.0
[INFO] [2020-12-08 15:01:30] Total Time: 1s
[INFO] [2020-12-08 15:01:30] Storing 3 Nodes
[INFO] [2020-12-08 15:01:30] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-08 15:01:30] Average Time: 0.0
[INFO] [2020-12-08 15:01:30] Total Time: 1s
[INFO] [2020-12-08 15:01:30] Storing 3 Occurrences
[INFO] [2020-12-08 15:01:30] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-08 15:01:30] Average Time: 0.0
[INFO] [2020-12-08 15:01:30] Total Time: 1s
[INFO] [2020-12-08 15:01:30] Storing 5 Traits
[INFO] [2020-12-08 15:01:30] Processing group of 5 in 1 groups of 1000
[INFO] [2020-12-08 15:01:30] Average Time: 0.01
[INFO] [2020-12-08 15:01:30] Total Time: 1s
[INFO] [2020-12-08 15:01:30] Storing 3 MetaTraits
[INFO] [2020-12-08 15:01:30] Processing group of 3 in 1 groups of 1000
[INFO] [2020-12-08 15:01:30] Average Time: 0.01
[INFO] [2020-12-08 15:01:30] Total Time: 1s
[STOP] [2020-12-08 15:01:30] parse_diff_and_store
[START] [2020-12-08 15:01:30] resolve_keys
[INFO] [2020-12-08 15:01:36] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-08 15:01:36] traits to occurrences...
[INFO] [2020-12-08 15:01:36] traits to nodes (through occurrences)...
[INFO] [2020-12-08 15:01:36] Traits to sex term...
[INFO] [2020-12-08 15:01:36] Traits to lifestage term...
[INFO] [2020-12-08 15:01:36] MetaTraits to traits...
[INFO] [2020-12-08 15:01:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-08 15:01:36] Assocs to occurrences...
[INFO] [2020-12-08 15:01:36] Assocs to nodes...
[INFO] [2020-12-08 15:01:36] Assoc to sex term...
[INFO] [2020-12-08 15:01:36] Assoc to lifestage term...
[INFO] [2020-12-08 15:01:36] MetaAssoc to assocs...
[STOP] [2020-12-08 15:01:36] resolve_keys
[START] [2020-12-08 15:01:36] hold_for_later_1
[STOP] [2020-12-08 15:01:36] hold_for_later_1
[START] [2020-12-08 15:01:36] hold_for_later_2
[STOP] [2020-12-08 15:01:36] hold_for_later_2
[START] [2020-12-08 15:01:36] resolve_missing_parents
[STOP] [2020-12-08 15:01:36] resolve_missing_parents
[START] [2020-12-08 15:01:36] rebuild_nodes
[START] [2020-12-08 15:01:36] Flattener#flatten
[START] [2020-12-08 15:01:36] Flattener#study_resource
[START] [2020-12-08 15:01:36] Flattener#build_ancestry
[STOP] [2020-12-08 15:01:36] Flattener#build_ancestry
[INFO] [2020-12-08 15:01:36] 3 ancestry keys
[START] [2020-12-08 15:01:36] build_node_ancestors
[INFO] [2020-12-08 15:01:36] old ancestors deleted.
[STOP] [2020-12-08 15:01:36] build_node_ancestors
[WARN] [2020-12-08 15:01:36] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-08 15:01:36] Flattener#flatten
[STOP] [2020-12-08 15:01:36] rebuild_nodes
[START] [2020-12-08 15:01:36] resolve_missing_media_owners
[STOP] [2020-12-08 15:01:36] resolve_missing_media_owners
[START] [2020-12-08 15:01:36] sanitize_media_verbatims
[STOP] [2020-12-08 15:01:36] sanitize_media_verbatims
[START] [2020-12-08 15:01:36] queue_downloads
[STOP] [2020-12-08 15:01:36] queue_downloads
[START] [2020-12-08 15:01:36] parse_names
[WARN] [2020-12-08 15:01:36] I see 3 names which still need to be parsed.
[STOP] [2020-12-08 15:01:37] parse_names
[START] [2020-12-08 15:01:37] denormalize_canonical_names_to_nodes
[STOP] [2020-12-08 15:01:37] denormalize_canonical_names_to_nodes
[START] [2020-12-08 15:01:37] match_nodes
[START] [2020-12-08 15:01:37] map_all_nodes_to_pages
[STOP] [2020-12-08 15:01:37] map_all_nodes_to_pages
[INFO] [2020-12-08 15:01:37] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2020-12-08 15:01:37] update_nodes
[STOP] [2020-12-08 15:01:37] update_nodes
[STOP] [2020-12-08 15:01:37] match_nodes
[START] [2020-12-08 15:01:37] reindex_search
[STOP] [2020-12-08 15:01:37] reindex_search
[START] [2020-12-08 15:01:37] normalize_units
[STOP] [2020-12-08 15:01:37] normalize_units
[START] [2020-12-08 15:01:37] calculate_statistics
[2020-12-08 15:01:37] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-08 15:01:37] calculate_statistics
[START] [2020-12-08 15:01:37] complete_harvest_instance
[START] [2020-12-08 15:01:37] overall_tsv_creation
[INFO] [2020-12-08 15:01:37] Processing group of 3 in 1 batches of 10000
[INFO] [2020-12-08 15:02:17] 3 Traits (unfiltered)...
[INFO] [2020-12-08 15:02:57] 3 Traits (filtered)...
[INFO] [2020-12-08 15:02:57] 0 Associations (filtered)...
[INFO] [2020-12-08 15:02:57] 5 metadata added.
[INFO] [2020-12-08 15:02:57] 0 metadata added.
[INFO] [2020-12-08 15:02:57] Average Time: 56.41
[INFO] [2020-12-08 15:02:57] Total Time: 1m20s
[STOP] [2020-12-08 15:02:57] overall_tsv_creation
[INFO] [2020-12-08 15:02:57] Done. Check your files:
[INFO] [2020-12-08 15:02:57] (3 lines) /app/public/data/rintoul_et_al_ri/publish_nodes.tsv
[INFO] [2020-12-08 15:02:57] (3 lines) /app/public/data/rintoul_et_al_ri/publish_scientific_names.tsv
[INFO] [2020-12-08 15:02:57] (4 lines) /app/public/data/rintoul_et_al_ri/publish_traits.tsv
[INFO] [2020-12-08 15:02:57] (6 lines) /app/public/data/rintoul_et_al_ri/publish_metadata.tsv
[STOP] [2020-12-08 15:02:57] complete_harvest_instance
[START] [2020-12-08 15:02:57] completed
[STOP] [2020-12-08 15:02:57] completed
[STOP] [2020-12-08 15:02:57] logged process, took 88.64
[INFO] [2021-04-19 16:47:42] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 16:56:22] ## remove_type: ScientificName
[INFO] [2021-04-19 16:56:22] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 16:56:22] [16:56:22.540] Removed 3 Scientificnames
[INFO] [2021-04-19 16:56:22] ## remove_type: Vernacular
[INFO] [2021-04-19 16:56:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:56:22] [16:56:22.541] Removed 0 Vernaculars
[INFO] [2021-04-19 16:56:22] ## remove_type: Article
[INFO] [2021-04-19 16:56:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:56:22] [16:56:22.542] Removed 0 Articles
[INFO] [2021-04-19 16:56:22] ## remove_type: Medium
[INFO] [2021-04-19 16:56:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:56:22] [16:56:22.544] Removed 0 Media
[INFO] [2021-04-19 16:56:22] ## remove_type: Trait
[INFO] [2021-04-19 16:56:22] ++ Calling delete_all on 5 instances...
[INFO] [2021-04-19 16:56:22] [16:56:22.546] Removed 5 Traits
[INFO] [2021-04-19 16:56:22] ## remove_type: MetaTrait
[INFO] [2021-04-19 16:56:22] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 16:56:22] [16:56:22.548] Removed 3 Metatraits
[INFO] [2021-04-19 16:56:22] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 16:56:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:56:22] [16:56:22.549] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 16:56:22] ## remove_type: Assoc
[INFO] [2021-04-19 16:56:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:56:22] [16:56:22.551] Removed 0 Assocs
[INFO] [2021-04-19 16:56:22] ## remove_type: MetaAssoc
[INFO] [2021-04-19 16:56:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:56:22] [16:56:22.552] Removed 0 Metaassocs
[INFO] [2021-04-19 16:56:22] ## remove_type: Identifier
[INFO] [2021-04-19 16:56:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:56:22] [16:56:22.554] Removed 0 Identifiers
[INFO] [2021-04-19 16:56:22] ## remove_type: Reference
[INFO] [2021-04-19 16:56:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:56:22] [16:56:22.555] Removed 0 References
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
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[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
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[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
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[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
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[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:22] Starting batch with ID 86121244...
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[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
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[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
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[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
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[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] Starting batch with ID 86121244...
[INFO] [2021-04-19 16:56:23] ## remove_type: Node
[INFO] [2021-04-19 16:56:23] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 16:56:23] [16:56:23.451] Removed 3 Nodes
[START] [2021-04-19 16:56:23] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:56:23] Creating resource from OpenData
[START] [2021-04-19 16:56:23] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:56:23] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:56:23] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:56:23] Creating resource from OpenData
[START] [2021-04-19 16:56:23] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:56:23] create_harvest_instance
[INFO] [2021-04-19 16:56:23] Created harvest instance #3810
[STOP] [2021-04-19 16:56:23] create_harvest_instance
[START] [2021-04-19 16:56:23] fetch_files
[STOP] [2021-04-19 16:56:23] fetch_files
[START] [2021-04-19 16:56:23] validate_each_file
[INFO] [2021-04-19 16:56:23] Looping over 3 formats...
[INFO] [2021-04-19 16:56:23] ...nodes (/app/public/data/rintoul_et_al_ri/taxa.txt)
[INFO] [2021-04-19 16:56:23] Valid: /app/public/converted_csv/rintoul_et_al_ri_nodes_3810.csv (3 lines)
[INFO] [2021-04-19 16:56:23] ...occurrences (/app/public/data/rintoul_et_al_ri/occurrences.txt)
[INFO] [2021-04-19 16:56:23] Valid: /app/public/converted_csv/rintoul_et_al_ri_occurrences_3810.csv (3 lines)
[INFO] [2021-04-19 16:56:23] ...measurements (/app/public/data/rintoul_et_al_ri/measurementsorfacts.txt)
[INFO] [2021-04-19 16:56:23] Valid: /app/public/converted_csv/rintoul_et_al_ri_measurements_3810.csv (5 lines)
[STOP] [2021-04-19 16:56:23] validate_each_file
[START] [2021-04-19 16:56:23] convert_to_csv
[INFO] [2021-04-19 16:56:23] Looping over 3 formats...
[INFO] [2021-04-19 16:56:23] ...nodes (/app/public/data/rintoul_et_al_ri/taxa.txt)
[CMD] [2021-04-19 16:56:23] /usr/bin/sort /app/public/converted_csv/rintoul_et_al_ri_nodes_3810.csv > /app/public/converted_csv/rintoul_et_al_ri_nodes_3810.csv_sorted
[INFO] [2021-04-19 16:56:23] Converted: /app/public/converted_csv/rintoul_et_al_ri_nodes_3810.csv (3 lines)
[INFO] [2021-04-19 16:56:23] ...occurrences (/app/public/data/rintoul_et_al_ri/occurrences.txt)
[CMD] [2021-04-19 16:56:23] /usr/bin/sort /app/public/converted_csv/rintoul_et_al_ri_occurrences_3810.csv > /app/public/converted_csv/rintoul_et_al_ri_occurrences_3810.csv_sorted
[INFO] [2021-04-19 16:56:23] Converted: /app/public/converted_csv/rintoul_et_al_ri_occurrences_3810.csv (3 lines)
[INFO] [2021-04-19 16:56:23] ...measurements (/app/public/data/rintoul_et_al_ri/measurementsorfacts.txt)
[CMD] [2021-04-19 16:56:23] /usr/bin/sort /app/public/converted_csv/rintoul_et_al_ri_measurements_3810.csv > /app/public/converted_csv/rintoul_et_al_ri_measurements_3810.csv_sorted
[INFO] [2021-04-19 16:56:23] Converted: /app/public/converted_csv/rintoul_et_al_ri_measurements_3810.csv (5 lines)
[STOP] [2021-04-19 16:56:23] convert_to_csv
[START] [2021-04-19 16:56:23] calculate_delta
[INFO] [2021-04-19 16:56:23] Looping over 3 formats...
[INFO] [2021-04-19 16:56:23] ...nodes (/app/public/data/rintoul_et_al_ri/taxa.txt)
[CMD] [2021-04-19 16:56:23] echo "0a" > /app/public/diff/rintoul_et_al_ri_nodes_3810.diff
[CMD] [2021-04-19 16:56:23] tail -n +1 /app/public/converted_csv/rintoul_et_al_ri_nodes_3810.csv >> /app/public/diff/rintoul_et_al_ri_nodes_3810.diff
[CMD] [2021-04-19 16:56:24] echo "." >> /app/public/diff/rintoul_et_al_ri_nodes_3810.diff
[INFO] [2021-04-19 16:56:24] Created diff: /app/public/diff/rintoul_et_al_ri_nodes_3810.diff (5 lines)
[INFO] [2021-04-19 16:56:24] ...occurrences (/app/public/data/rintoul_et_al_ri/occurrences.txt)
[CMD] [2021-04-19 16:56:24] echo "0a" > /app/public/diff/rintoul_et_al_ri_occurrences_3810.diff
[CMD] [2021-04-19 16:56:24] tail -n +1 /app/public/converted_csv/rintoul_et_al_ri_occurrences_3810.csv >> /app/public/diff/rintoul_et_al_ri_occurrences_3810.diff
[CMD] [2021-04-19 16:56:24] echo "." >> /app/public/diff/rintoul_et_al_ri_occurrences_3810.diff
[INFO] [2021-04-19 16:56:24] Created diff: /app/public/diff/rintoul_et_al_ri_occurrences_3810.diff (5 lines)
[INFO] [2021-04-19 16:56:24] ...measurements (/app/public/data/rintoul_et_al_ri/measurementsorfacts.txt)
[CMD] [2021-04-19 16:56:24] echo "0a" > /app/public/diff/rintoul_et_al_ri_measurements_3810.diff
[CMD] [2021-04-19 16:56:24] tail -n +1 /app/public/converted_csv/rintoul_et_al_ri_measurements_3810.csv >> /app/public/diff/rintoul_et_al_ri_measurements_3810.diff
[CMD] [2021-04-19 16:56:24] echo "." >> /app/public/diff/rintoul_et_al_ri_measurements_3810.diff
[INFO] [2021-04-19 16:56:24] Created diff: /app/public/diff/rintoul_et_al_ri_measurements_3810.diff (7 lines)
[STOP] [2021-04-19 16:56:24] calculate_delta
[START] [2021-04-19 16:56:24] parse_diff_and_store
[INFO] [2021-04-19 16:56:24] Handling diff: /app/public/diff/rintoul_et_al_ri_nodes_3810.diff (5 lines)
[INFO] [2021-04-19 16:56:24] Loading nodes diff file into memory (5 /app/public/diff/rintoul_et_al_ri_nodes_3810.diff lines)...
[INFO] [2021-04-19 16:56:24] Handling diff: /app/public/diff/rintoul_et_al_ri_occurrences_3810.diff (5 lines)
[INFO] [2021-04-19 16:56:24] Loading occurrences diff file into memory (5 /app/public/diff/rintoul_et_al_ri_occurrences_3810.diff lines)...
[INFO] [2021-04-19 16:56:24] Handling diff: /app/public/diff/rintoul_et_al_ri_measurements_3810.diff (7 lines)
[INFO] [2021-04-19 16:56:24] Loading measurements diff file into memory (7 /app/public/diff/rintoul_et_al_ri_measurements_3810.diff lines)...
[INFO] [2021-04-19 16:56:24] Storing 3 ScientificNames
[INFO] [2021-04-19 16:56:24] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 16:56:24] Average Time: 0.0
[INFO] [2021-04-19 16:56:24] Total Time: 1s
[INFO] [2021-04-19 16:56:24] Storing 3 Nodes
[INFO] [2021-04-19 16:56:24] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 16:56:24] Average Time: 0.0
[INFO] [2021-04-19 16:56:24] Total Time: 1s
[INFO] [2021-04-19 16:56:24] Storing 3 Occurrences
[INFO] [2021-04-19 16:56:24] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 16:56:24] Average Time: 0.0
[INFO] [2021-04-19 16:56:24] Total Time: 1s
[INFO] [2021-04-19 16:56:24] Storing 5 Traits
[INFO] [2021-04-19 16:56:24] Processing group of 5 in 1 groups of 1000
[INFO] [2021-04-19 16:56:24] Average Time: 0.0
[INFO] [2021-04-19 16:56:24] Total Time: 1s
[INFO] [2021-04-19 16:56:24] Storing 3 MetaTraits
[INFO] [2021-04-19 16:56:24] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 16:56:24] Average Time: 0.0
[INFO] [2021-04-19 16:56:24] Total Time: 1s
[STOP] [2021-04-19 16:56:24] parse_diff_and_store
[START] [2021-04-19 16:56:24] resolve_keys
[INFO] [2021-04-19 16:56:30] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 16:56:30] traits to occurrences...
[INFO] [2021-04-19 16:56:30] traits to nodes (through occurrences)...
[INFO] [2021-04-19 16:56:30] Traits to sex term...
[INFO] [2021-04-19 16:56:30] Traits to lifestage term...
[INFO] [2021-04-19 16:56:30] MetaTraits to traits...
[INFO] [2021-04-19 16:56:30] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 16:56:30] Assocs to occurrences...
[INFO] [2021-04-19 16:56:30] Assocs to nodes...
[INFO] [2021-04-19 16:56:30] Assoc to sex term...
[INFO] [2021-04-19 16:56:30] Assoc to lifestage term...
[INFO] [2021-04-19 16:56:30] MetaAssoc to assocs...
[STOP] [2021-04-19 16:56:30] resolve_keys
[START] [2021-04-19 16:56:30] hold_for_later_1
[STOP] [2021-04-19 16:56:30] hold_for_later_1
[START] [2021-04-19 16:56:30] hold_for_later_2
[STOP] [2021-04-19 16:56:30] hold_for_later_2
[START] [2021-04-19 16:56:30] resolve_missing_parents
[STOP] [2021-04-19 16:56:30] resolve_missing_parents
[START] [2021-04-19 16:56:30] rebuild_nodes
[START] [2021-04-19 16:56:30] Flattener#flatten
[START] [2021-04-19 16:56:30] Flattener#study_resource
[START] [2021-04-19 16:56:30] Flattener#build_ancestry
[STOP] [2021-04-19 16:56:30] Flattener#build_ancestry
[INFO] [2021-04-19 16:56:30] 3 ancestry keys
[START] [2021-04-19 16:56:30] build_node_ancestors
[INFO] [2021-04-19 16:56:30] old ancestors deleted.
[STOP] [2021-04-19 16:56:30] build_node_ancestors
[WARN] [2021-04-19 16:56:30] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 16:56:30] Flattener#flatten
[STOP] [2021-04-19 16:56:30] rebuild_nodes
[START] [2021-04-19 16:56:30] resolve_missing_media_owners
[STOP] [2021-04-19 16:56:30] resolve_missing_media_owners
[START] [2021-04-19 16:56:30] sanitize_media_verbatims
[STOP] [2021-04-19 16:56:30] sanitize_media_verbatims
[START] [2021-04-19 16:56:30] queue_downloads
[STOP] [2021-04-19 16:56:30] queue_downloads
[START] [2021-04-19 16:56:30] parse_names
[WARN] [2021-04-19 16:56:30] I see 3 names which still need to be parsed.
[STOP] [2021-04-19 16:56:31] parse_names
[START] [2021-04-19 16:56:31] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 16:56:31] denormalize_canonical_names_to_nodes
[START] [2021-04-19 16:56:31] match_nodes
[START] [2021-04-19 16:56:31] map_all_nodes_to_pages
[STOP] [2021-04-19 16:56:31] map_all_nodes_to_pages
[INFO] [2021-04-19 16:56:31] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2021-04-19 16:56:31] update_nodes
[STOP] [2021-04-19 16:56:31] update_nodes
[STOP] [2021-04-19 16:56:31] match_nodes
[START] [2021-04-19 16:56:31] reindex_search
[STOP] [2021-04-19 16:56:31] reindex_search
[START] [2021-04-19 16:56:31] normalize_units
[STOP] [2021-04-19 16:56:31] normalize_units
[START] [2021-04-19 16:56:31] calculate_statistics
[2021-04-19 16:56:31] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 16:56:31] calculate_statistics
[START] [2021-04-19 16:56:31] complete_harvest_instance
[START] [2021-04-19 16:56:31] overall_tsv_creation
[INFO] [2021-04-19 16:56:31] Processing group of 3 in 1 batches of 10000
[INFO] [2021-04-19 16:57:07] 3 Traits (unfiltered)...
[INFO] [2021-04-19 16:57:40] 3 Traits (filtered)...
[INFO] [2021-04-19 16:57:40] 0 Associations (filtered)...
[INFO] [2021-04-19 16:57:40] 2 metadata added.
[INFO] [2021-04-19 16:57:40] 0 metadata added.
[INFO] [2021-04-19 16:58:06] Average Time: 71.58
[INFO] [2021-04-19 16:58:06] Total Time: 1m36s
[STOP] [2021-04-19 16:58:06] overall_tsv_creation
[INFO] [2021-04-19 16:58:06] Done. Check your files:
[INFO] [2021-04-19 16:58:06] (3 lines) /app/public/data/rintoul_et_al_ri/publish_nodes.tsv
[INFO] [2021-04-19 16:58:06] (3 lines) /app/public/data/rintoul_et_al_ri/publish_scientific_names.tsv
[INFO] [2021-04-19 16:58:06] (4 lines) /app/public/data/rintoul_et_al_ri/publish_traits.tsv
[INFO] [2021-04-19 16:58:06] (3 lines) /app/public/data/rintoul_et_al_ri/publish_metadata.tsv
[STOP] [2021-04-19 16:58:06] complete_harvest_instance
[START] [2021-04-19 16:58:06] completed
[STOP] [2021-04-19 16:58:06] completed
[STOP] [2021-04-19 16:58:06] logged process, took 103.1
Latest Process