Harvest for Elofsson 1965 Created 19 Apr 15:16

Harvesting Log

# Logfile created on 2020-08-27 15:35:27 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:35:27] logged process
[START] [2020-08-27 15:35:27] Creating resource from OpenData
[START] [2020-08-27 15:35:27] logged process
[START] [2020-08-27 15:35:27] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:35:28] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:35:28] Creating resource from OpenData
[INFO] [2020-11-19 13:54:04] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 13:54:04] ## remove_type: ScientificName
[INFO] [2020-11-19 13:54:04] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:54:04] [13:54:04.478] Removed 0 Scientificnames
[INFO] [2020-11-19 13:54:04] ## remove_type: Vernacular
[INFO] [2020-11-19 13:54:04] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:54:04] [13:54:04.480] Removed 0 Vernaculars
[INFO] [2020-11-19 13:54:04] ## remove_type: Article
[INFO] [2020-11-19 13:54:04] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:54:04] [13:54:04.483] Removed 0 Articles
[INFO] [2020-11-19 13:54:04] ## remove_type: Medium
[INFO] [2020-11-19 13:54:04] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:54:04] [13:54:04.486] Removed 0 Media
[INFO] [2020-11-19 13:54:04] ## remove_type: Trait
[INFO] [2020-11-19 13:54:04] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:54:04] [13:54:04.488] Removed 0 Traits
[INFO] [2020-11-19 13:54:04] ## remove_type: MetaTrait
[INFO] [2020-11-19 13:54:04] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:54:04] [13:54:04.491] Removed 0 Metatraits
[INFO] [2020-11-19 13:54:04] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 13:54:04] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:54:04] [13:54:04.493] Removed 0 Occurrencemetadata
[INFO] [2020-11-19 13:54:04] ## remove_type: Assoc
[INFO] [2020-11-19 13:54:04] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:54:04] [13:54:04.496] Removed 0 Assocs
[INFO] [2020-11-19 13:54:04] ## remove_type: MetaAssoc
[INFO] [2020-11-19 13:54:04] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:54:04] [13:54:04.499] Removed 0 Metaassocs
[INFO] [2020-11-19 13:54:04] ## remove_type: Identifier
[INFO] [2020-11-19 13:54:04] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:54:04] [13:54:04.502] Removed 0 Identifiers
[INFO] [2020-11-19 13:54:04] ## remove_type: Reference
[INFO] [2020-11-19 13:54:04] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:54:04] [13:54:04.504] Removed 0 References
[INFO] [2020-11-19 13:54:04] ## remove_type: Node
[INFO] [2020-11-19 13:54:04] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:54:04] [13:54:04.524] Removed 0 Nodes
[START] [2020-11-19 13:54:04] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:54:04] Creating resource from OpenData
[START] [2020-11-19 13:54:04] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:54:04] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:54:04] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:54:04] Creating resource from OpenData
[START] [2020-11-19 13:54:04] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:54:04] create_harvest_instance
[STOP] [2020-11-19 13:54:06] create_harvest_instance
[START] [2020-11-19 13:54:06] fetch_files
[STOP] [2020-11-19 13:54:06] fetch_files
[START] [2020-11-19 13:54:06] validate_each_file
[STOP] [2020-11-19 13:54:06] validate_each_file
[START] [2020-11-19 13:54:06] convert_to_csv
[CMD] [2020-11-19 13:54:06] /usr/bin/sort /app/public/converted_csv/elofsson_elofsso_refs_24478.csv > /app/public/converted_csv/elofsson_elofsso_refs_24478.csv_sorted
[CMD] [2020-11-19 13:54:06] /usr/bin/sort /app/public/converted_csv/elofsson_elofsso_nodes_24479.csv > /app/public/converted_csv/elofsson_elofsso_nodes_24479.csv_sorted
[CMD] [2020-11-19 13:54:06] /usr/bin/sort /app/public/converted_csv/elofsson_elofsso_occurrences_24480.csv > /app/public/converted_csv/elofsson_elofsso_occurrences_24480.csv_sorted
[CMD] [2020-11-19 13:54:06] /usr/bin/sort /app/public/converted_csv/elofsson_elofsso_measurements_24481.csv > /app/public/converted_csv/elofsson_elofsso_measurements_24481.csv_sorted
[STOP] [2020-11-19 13:54:06] convert_to_csv
[START] [2020-11-19 13:54:06] calculate_delta
[CMD] [2020-11-19 13:54:06] echo "0a" > /app/public/diff/elofsson_elofsso_refs_24478.diff
[CMD] [2020-11-19 13:54:06] tail -n +1 /app/public/converted_csv/elofsson_elofsso_refs_24478.csv >> /app/public/diff/elofsson_elofsso_refs_24478.diff
[CMD] [2020-11-19 13:54:06] echo "." >> /app/public/diff/elofsson_elofsso_refs_24478.diff
[CMD] [2020-11-19 13:54:06] echo "0a" > /app/public/diff/elofsson_elofsso_nodes_24479.diff
[CMD] [2020-11-19 13:54:06] tail -n +1 /app/public/converted_csv/elofsson_elofsso_nodes_24479.csv >> /app/public/diff/elofsson_elofsso_nodes_24479.diff
[CMD] [2020-11-19 13:54:06] echo "." >> /app/public/diff/elofsson_elofsso_nodes_24479.diff
[CMD] [2020-11-19 13:54:06] echo "0a" > /app/public/diff/elofsson_elofsso_occurrences_24480.diff
[CMD] [2020-11-19 13:54:06] tail -n +1 /app/public/converted_csv/elofsson_elofsso_occurrences_24480.csv >> /app/public/diff/elofsson_elofsso_occurrences_24480.diff
[CMD] [2020-11-19 13:54:06] echo "." >> /app/public/diff/elofsson_elofsso_occurrences_24480.diff
[CMD] [2020-11-19 13:54:06] echo "0a" > /app/public/diff/elofsson_elofsso_measurements_24481.diff
[CMD] [2020-11-19 13:54:06] tail -n +1 /app/public/converted_csv/elofsson_elofsso_measurements_24481.csv >> /app/public/diff/elofsson_elofsso_measurements_24481.diff
[CMD] [2020-11-19 13:54:06] echo "." >> /app/public/diff/elofsson_elofsso_measurements_24481.diff
[STOP] [2020-11-19 13:54:06] calculate_delta
[START] [2020-11-19 13:54:06] parse_diff_and_store
[INFO] [2020-11-19 13:54:06] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 13:54:06] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 13:54:06] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 13:54:06] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-19 13:54:07] Storing 3 ScientificNames
[INFO] [2020-11-19 13:54:07] Processing group of 3 in 1 groups of 1000
[INFO] [2020-11-19 13:54:07] Average Time: 0.0
[INFO] [2020-11-19 13:54:07] Total Time: 1s
[INFO] [2020-11-19 13:54:07] Storing 3 Nodes
[INFO] [2020-11-19 13:54:07] Processing group of 3 in 1 groups of 1000
[INFO] [2020-11-19 13:54:07] Average Time: 0.0
[INFO] [2020-11-19 13:54:07] Total Time: 1s
[INFO] [2020-11-19 13:54:07] Storing 3 Occurrences
[INFO] [2020-11-19 13:54:07] Processing group of 3 in 1 groups of 1000
[INFO] [2020-11-19 13:54:07] Average Time: 0.0
[INFO] [2020-11-19 13:54:07] Total Time: 1s
[INFO] [2020-11-19 13:54:07] Storing 6 Traits
[INFO] [2020-11-19 13:54:07] Processing group of 6 in 1 groups of 1000
[INFO] [2020-11-19 13:54:07] Average Time: 0.03
[INFO] [2020-11-19 13:54:07] Total Time: 1s
[INFO] [2020-11-19 13:54:07] Storing 6 MetaTraits
[INFO] [2020-11-19 13:54:07] Processing group of 6 in 1 groups of 1000
[INFO] [2020-11-19 13:54:07] Average Time: 0.0
[INFO] [2020-11-19 13:54:07] Total Time: 1s
[STOP] [2020-11-19 13:54:07] parse_diff_and_store
[START] [2020-11-19 13:54:07] resolve_keys
[INFO] [2020-11-19 13:54:13] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-19 13:54:13] traits to occurrences...
[INFO] [2020-11-19 13:54:13] traits to nodes (through occurrences)...
[INFO] [2020-11-19 13:54:13] Traits to sex term...
[INFO] [2020-11-19 13:54:13] Traits to lifestage term...
[INFO] [2020-11-19 13:54:13] MetaTraits to traits...
[INFO] [2020-11-19 13:54:13] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-19 13:54:13] Assocs to occurrences...
[INFO] [2020-11-19 13:54:13] Assocs to nodes...
[INFO] [2020-11-19 13:54:13] Assoc to sex term...
[INFO] [2020-11-19 13:54:13] Assoc to lifestage term...
[INFO] [2020-11-19 13:54:13] MetaAssoc to assocs...
[STOP] [2020-11-19 13:54:13] resolve_keys
[START] [2020-11-19 13:54:13] hold_for_later_1
[STOP] [2020-11-19 13:54:13] hold_for_later_1
[START] [2020-11-19 13:54:13] hold_for_later_2
[STOP] [2020-11-19 13:54:13] hold_for_later_2
[START] [2020-11-19 13:54:13] resolve_missing_parents
[STOP] [2020-11-19 13:54:13] resolve_missing_parents
[START] [2020-11-19 13:54:13] rebuild_nodes
[START] [2020-11-19 13:54:13] Flattener#flatten
[START] [2020-11-19 13:54:13] Flattener#study_resource
[START] [2020-11-19 13:54:13] Flattener#build_ancestry
[STOP] [2020-11-19 13:54:13] Flattener#build_ancestry
[INFO] [2020-11-19 13:54:13] 3 ancestry keys
[START] [2020-11-19 13:54:13] build_node_ancestors
[INFO] [2020-11-19 13:54:13] old ancestors deleted.
[STOP] [2020-11-19 13:54:13] build_node_ancestors
[WARN] [2020-11-19 13:54:13] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-19 13:54:13] Flattener#flatten
[STOP] [2020-11-19 13:54:13] rebuild_nodes
[START] [2020-11-19 13:54:13] resolve_missing_media_owners
[STOP] [2020-11-19 13:54:13] resolve_missing_media_owners
[START] [2020-11-19 13:54:13] sanitize_media_verbatims
[STOP] [2020-11-19 13:54:13] sanitize_media_verbatims
[START] [2020-11-19 13:54:13] queue_downloads
[STOP] [2020-11-19 13:54:13] queue_downloads
[START] [2020-11-19 13:54:13] parse_names
[WARN] [2020-11-19 13:54:13] I see 3 names which still need to be parsed.
[STOP] [2020-11-19 13:54:15] parse_names
[START] [2020-11-19 13:54:15] denormalize_canonical_names_to_nodes
[STOP] [2020-11-19 13:54:15] denormalize_canonical_names_to_nodes
[START] [2020-11-19 13:54:15] match_nodes
[START] [2020-11-19 13:54:15] map_all_nodes_to_pages
[STOP] [2020-11-19 13:54:15] map_all_nodes_to_pages
[INFO] [2020-11-19 13:54:15] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2020-11-19 13:54:15] update_nodes
[STOP] [2020-11-19 13:54:15] update_nodes
[STOP] [2020-11-19 13:54:15] match_nodes
[START] [2020-11-19 13:54:15] reindex_search
[STOP] [2020-11-19 13:54:15] reindex_search
[START] [2020-11-19 13:54:15] normalize_units
[STOP] [2020-11-19 13:54:15] normalize_units
[START] [2020-11-19 13:54:15] calculate_statistics
[2020-11-19 13:54:15] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-19 13:54:15] calculate_statistics
[START] [2020-11-19 13:54:15] complete_harvest_instance
[START] [2020-11-19 13:54:15] overall_tsv_creation
[INFO] [2020-11-19 13:54:15] Processing group of 3 in 1 batches of 10000
[INFO] [2020-11-19 13:54:58] 3 Traits (unfiltered)...
[INFO] [2020-11-19 13:55:43] 3 Traits (filtered)...
[INFO] [2020-11-19 13:55:43] 0 Associations (filtered)...
[INFO] [2020-11-19 13:55:44] 9 metadata added.
[INFO] [2020-11-19 13:55:44] 0 metadata added.
[INFO] [2020-11-19 13:55:44] Average Time: 69.16
[INFO] [2020-11-19 13:55:44] Total Time: 1m29s
[STOP] [2020-11-19 13:55:44] overall_tsv_creation
[INFO] [2020-11-19 13:55:44] Done. Check your files:
[INFO] [2020-11-19 13:55:44] (3 lines) /app/public/data/elofsson_elofsso/publish_nodes.tsv
[INFO] [2020-11-19 13:55:44] (3 lines) /app/public/data/elofsson_elofsso/publish_scientific_names.tsv
[INFO] [2020-11-19 13:55:44] (4 lines) /app/public/data/elofsson_elofsso/publish_traits.tsv
[INFO] [2020-11-19 13:55:44] (10 lines) /app/public/data/elofsson_elofsso/publish_metadata.tsv
[STOP] [2020-11-19 13:55:44] complete_harvest_instance
[START] [2020-11-19 13:55:44] completed
[STOP] [2020-11-19 13:55:44] completed
[STOP] [2020-11-19 13:55:44] logged process, took 99.22
[INFO] [2021-04-19 15:14:36] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:16:17] ## remove_type: ScientificName
[INFO] [2021-04-19 15:16:17] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 15:16:17] [15:16:17.616] Removed 3 Scientificnames
[INFO] [2021-04-19 15:16:17] ## remove_type: Vernacular
[INFO] [2021-04-19 15:16:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:16:17] [15:16:17.618] Removed 0 Vernaculars
[INFO] [2021-04-19 15:16:17] ## remove_type: Article
[INFO] [2021-04-19 15:16:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:16:17] [15:16:17.619] Removed 0 Articles
[INFO] [2021-04-19 15:16:17] ## remove_type: Medium
[INFO] [2021-04-19 15:16:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:16:17] [15:16:17.621] Removed 0 Media
[INFO] [2021-04-19 15:16:17] ## remove_type: Trait
[INFO] [2021-04-19 15:16:17] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 15:16:17] [15:16:17.623] Removed 6 Traits
[INFO] [2021-04-19 15:16:17] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:16:17] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 15:16:17] [15:16:17.625] Removed 6 Metatraits
[INFO] [2021-04-19 15:16:17] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:16:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:16:17] [15:16:17.626] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:16:17] ## remove_type: Assoc
[INFO] [2021-04-19 15:16:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:16:17] [15:16:17.627] Removed 0 Assocs
[INFO] [2021-04-19 15:16:17] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:16:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:16:17] [15:16:17.629] Removed 0 Metaassocs
[INFO] [2021-04-19 15:16:17] ## remove_type: Identifier
[INFO] [2021-04-19 15:16:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:16:17] [15:16:17.630] Removed 0 Identifiers
[INFO] [2021-04-19 15:16:17] ## remove_type: Reference
[INFO] [2021-04-19 15:16:17] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:16:17] [15:16:17.631] Removed 0 References
[INFO] [2021-04-19 15:16:17] Starting batch with ID 84620788...
[INFO] [2021-04-19 15:16:17] Starting batch with ID 84620788...
[INFO] [2021-04-19 15:16:17] Starting batch with ID 84620788...
[INFO] [2021-04-19 15:16:17] Starting batch with ID 84620788...
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[INFO] [2021-04-19 15:16:18] Starting batch with ID 84620788...
[INFO] [2021-04-19 15:16:18] Starting batch with ID 84620788...
[INFO] [2021-04-19 15:16:18] Starting batch with ID 84620788...
[INFO] [2021-04-19 15:16:18] Starting batch with ID 84620788...
[INFO] [2021-04-19 15:16:18] Starting batch with ID 84620789...
[INFO] [2021-04-19 15:16:18] ## remove_type: Node
[INFO] [2021-04-19 15:16:18] ++ Calling delete_all on 3 instances...
[INFO] [2021-04-19 15:16:18] [15:16:18.179] Removed 3 Nodes
[START] [2021-04-19 15:16:18] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:16:18] Creating resource from OpenData
[START] [2021-04-19 15:16:18] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:16:18] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:16:18] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:16:18] Creating resource from OpenData
[START] [2021-04-19 15:16:18] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:16:18] create_harvest_instance
[INFO] [2021-04-19 15:16:18] Created harvest instance #3760
[STOP] [2021-04-19 15:16:18] create_harvest_instance
[START] [2021-04-19 15:16:18] fetch_files
[STOP] [2021-04-19 15:16:18] fetch_files
[START] [2021-04-19 15:16:18] validate_each_file
[INFO] [2021-04-19 15:16:18] Looping over 4 formats...
[INFO] [2021-04-19 15:16:18] ...refs (/app/public/data/elofsson_elofsso/references.tsv)
[INFO] [2021-04-19 15:16:18] Valid: /app/public/converted_csv/elofsson_elofsso_refs_3760.csv (0 lines)
[INFO] [2021-04-19 15:16:18] ...nodes (/app/public/data/elofsson_elofsso/taxa.txt)
[INFO] [2021-04-19 15:16:18] Valid: /app/public/converted_csv/elofsson_elofsso_nodes_3760.csv (3 lines)
[INFO] [2021-04-19 15:16:18] ...occurrences (/app/public/data/elofsson_elofsso/occurrences.txt)
[INFO] [2021-04-19 15:16:18] Valid: /app/public/converted_csv/elofsson_elofsso_occurrences_3760.csv (3 lines)
[INFO] [2021-04-19 15:16:18] ...measurements (/app/public/data/elofsson_elofsso/measurementsorfacts.txt)
[INFO] [2021-04-19 15:16:18] Valid: /app/public/converted_csv/elofsson_elofsso_measurements_3760.csv (6 lines)
[STOP] [2021-04-19 15:16:18] validate_each_file
[START] [2021-04-19 15:16:18] convert_to_csv
[INFO] [2021-04-19 15:16:18] Looping over 4 formats...
[INFO] [2021-04-19 15:16:18] ...refs (/app/public/data/elofsson_elofsso/references.tsv)
[CMD] [2021-04-19 15:16:18] /usr/bin/sort /app/public/converted_csv/elofsson_elofsso_refs_3760.csv > /app/public/converted_csv/elofsson_elofsso_refs_3760.csv_sorted
[INFO] [2021-04-19 15:16:18] Converted: /app/public/converted_csv/elofsson_elofsso_refs_3760.csv (0 lines)
[INFO] [2021-04-19 15:16:18] ...nodes (/app/public/data/elofsson_elofsso/taxa.txt)
[CMD] [2021-04-19 15:16:18] /usr/bin/sort /app/public/converted_csv/elofsson_elofsso_nodes_3760.csv > /app/public/converted_csv/elofsson_elofsso_nodes_3760.csv_sorted
[INFO] [2021-04-19 15:16:18] Converted: /app/public/converted_csv/elofsson_elofsso_nodes_3760.csv (3 lines)
[INFO] [2021-04-19 15:16:18] ...occurrences (/app/public/data/elofsson_elofsso/occurrences.txt)
[CMD] [2021-04-19 15:16:18] /usr/bin/sort /app/public/converted_csv/elofsson_elofsso_occurrences_3760.csv > /app/public/converted_csv/elofsson_elofsso_occurrences_3760.csv_sorted
[INFO] [2021-04-19 15:16:18] Converted: /app/public/converted_csv/elofsson_elofsso_occurrences_3760.csv (3 lines)
[INFO] [2021-04-19 15:16:18] ...measurements (/app/public/data/elofsson_elofsso/measurementsorfacts.txt)
[CMD] [2021-04-19 15:16:18] /usr/bin/sort /app/public/converted_csv/elofsson_elofsso_measurements_3760.csv > /app/public/converted_csv/elofsson_elofsso_measurements_3760.csv_sorted
[INFO] [2021-04-19 15:16:18] Converted: /app/public/converted_csv/elofsson_elofsso_measurements_3760.csv (6 lines)
[STOP] [2021-04-19 15:16:18] convert_to_csv
[START] [2021-04-19 15:16:18] calculate_delta
[INFO] [2021-04-19 15:16:18] Looping over 4 formats...
[INFO] [2021-04-19 15:16:18] ...refs (/app/public/data/elofsson_elofsso/references.tsv)
[CMD] [2021-04-19 15:16:18] echo "0a" > /app/public/diff/elofsson_elofsso_refs_3760.diff
[CMD] [2021-04-19 15:16:18] tail -n +1 /app/public/converted_csv/elofsson_elofsso_refs_3760.csv >> /app/public/diff/elofsson_elofsso_refs_3760.diff
[CMD] [2021-04-19 15:16:18] echo "." >> /app/public/diff/elofsson_elofsso_refs_3760.diff
[INFO] [2021-04-19 15:16:18] Created diff: /app/public/diff/elofsson_elofsso_refs_3760.diff (2 lines)
[INFO] [2021-04-19 15:16:18] ...nodes (/app/public/data/elofsson_elofsso/taxa.txt)
[CMD] [2021-04-19 15:16:18] echo "0a" > /app/public/diff/elofsson_elofsso_nodes_3760.diff
[CMD] [2021-04-19 15:16:18] tail -n +1 /app/public/converted_csv/elofsson_elofsso_nodes_3760.csv >> /app/public/diff/elofsson_elofsso_nodes_3760.diff
[CMD] [2021-04-19 15:16:18] echo "." >> /app/public/diff/elofsson_elofsso_nodes_3760.diff
[INFO] [2021-04-19 15:16:18] Created diff: /app/public/diff/elofsson_elofsso_nodes_3760.diff (5 lines)
[INFO] [2021-04-19 15:16:18] ...occurrences (/app/public/data/elofsson_elofsso/occurrences.txt)
[CMD] [2021-04-19 15:16:18] echo "0a" > /app/public/diff/elofsson_elofsso_occurrences_3760.diff
[CMD] [2021-04-19 15:16:18] tail -n +1 /app/public/converted_csv/elofsson_elofsso_occurrences_3760.csv >> /app/public/diff/elofsson_elofsso_occurrences_3760.diff
[CMD] [2021-04-19 15:16:18] echo "." >> /app/public/diff/elofsson_elofsso_occurrences_3760.diff
[INFO] [2021-04-19 15:16:18] Created diff: /app/public/diff/elofsson_elofsso_occurrences_3760.diff (5 lines)
[INFO] [2021-04-19 15:16:18] ...measurements (/app/public/data/elofsson_elofsso/measurementsorfacts.txt)
[CMD] [2021-04-19 15:16:18] echo "0a" > /app/public/diff/elofsson_elofsso_measurements_3760.diff
[CMD] [2021-04-19 15:16:18] tail -n +1 /app/public/converted_csv/elofsson_elofsso_measurements_3760.csv >> /app/public/diff/elofsson_elofsso_measurements_3760.diff
[CMD] [2021-04-19 15:16:18] echo "." >> /app/public/diff/elofsson_elofsso_measurements_3760.diff
[INFO] [2021-04-19 15:16:18] Created diff: /app/public/diff/elofsson_elofsso_measurements_3760.diff (8 lines)
[STOP] [2021-04-19 15:16:18] calculate_delta
[START] [2021-04-19 15:16:18] parse_diff_and_store
[INFO] [2021-04-19 15:16:18] Handling diff: /app/public/diff/elofsson_elofsso_refs_3760.diff (2 lines)
[INFO] [2021-04-19 15:16:18] Loading refs diff file into memory (2 /app/public/diff/elofsson_elofsso_refs_3760.diff lines)...
[INFO] [2021-04-19 15:16:18] Handling diff: /app/public/diff/elofsson_elofsso_nodes_3760.diff (5 lines)
[INFO] [2021-04-19 15:16:18] Loading nodes diff file into memory (5 /app/public/diff/elofsson_elofsso_nodes_3760.diff lines)...
[INFO] [2021-04-19 15:16:18] Handling diff: /app/public/diff/elofsson_elofsso_occurrences_3760.diff (5 lines)
[INFO] [2021-04-19 15:16:18] Loading occurrences diff file into memory (5 /app/public/diff/elofsson_elofsso_occurrences_3760.diff lines)...
[INFO] [2021-04-19 15:16:19] Handling diff: /app/public/diff/elofsson_elofsso_measurements_3760.diff (8 lines)
[INFO] [2021-04-19 15:16:19] Loading measurements diff file into memory (8 /app/public/diff/elofsson_elofsso_measurements_3760.diff lines)...
[INFO] [2021-04-19 15:16:19] Storing 3 ScientificNames
[INFO] [2021-04-19 15:16:19] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 15:16:19] Average Time: 0.0
[INFO] [2021-04-19 15:16:19] Total Time: 1s
[INFO] [2021-04-19 15:16:19] Storing 3 Nodes
[INFO] [2021-04-19 15:16:19] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 15:16:19] Average Time: 0.0
[INFO] [2021-04-19 15:16:19] Total Time: 1s
[INFO] [2021-04-19 15:16:19] Storing 3 Occurrences
[INFO] [2021-04-19 15:16:19] Processing group of 3 in 1 groups of 1000
[INFO] [2021-04-19 15:16:19] Average Time: 0.0
[INFO] [2021-04-19 15:16:19] Total Time: 1s
[INFO] [2021-04-19 15:16:19] Storing 6 Traits
[INFO] [2021-04-19 15:16:19] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 15:16:19] Average Time: 0.0
[INFO] [2021-04-19 15:16:19] Total Time: 1s
[INFO] [2021-04-19 15:16:19] Storing 6 MetaTraits
[INFO] [2021-04-19 15:16:19] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 15:16:19] Average Time: 0.0
[INFO] [2021-04-19 15:16:19] Total Time: 1s
[STOP] [2021-04-19 15:16:19] parse_diff_and_store
[START] [2021-04-19 15:16:19] resolve_keys
[INFO] [2021-04-19 15:16:24] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:16:24] traits to occurrences...
[INFO] [2021-04-19 15:16:24] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:16:24] Traits to sex term...
[INFO] [2021-04-19 15:16:24] Traits to lifestage term...
[INFO] [2021-04-19 15:16:24] MetaTraits to traits...
[INFO] [2021-04-19 15:16:24] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:16:25] Assocs to occurrences...
[INFO] [2021-04-19 15:16:25] Assocs to nodes...
[INFO] [2021-04-19 15:16:25] Assoc to sex term...
[INFO] [2021-04-19 15:16:25] Assoc to lifestage term...
[INFO] [2021-04-19 15:16:25] MetaAssoc to assocs...
[STOP] [2021-04-19 15:16:25] resolve_keys
[START] [2021-04-19 15:16:25] hold_for_later_1
[STOP] [2021-04-19 15:16:25] hold_for_later_1
[START] [2021-04-19 15:16:25] hold_for_later_2
[STOP] [2021-04-19 15:16:25] hold_for_later_2
[START] [2021-04-19 15:16:25] resolve_missing_parents
[STOP] [2021-04-19 15:16:25] resolve_missing_parents
[START] [2021-04-19 15:16:25] rebuild_nodes
[START] [2021-04-19 15:16:25] Flattener#flatten
[START] [2021-04-19 15:16:25] Flattener#study_resource
[START] [2021-04-19 15:16:25] Flattener#build_ancestry
[STOP] [2021-04-19 15:16:25] Flattener#build_ancestry
[INFO] [2021-04-19 15:16:25] 3 ancestry keys
[START] [2021-04-19 15:16:25] build_node_ancestors
[INFO] [2021-04-19 15:16:25] old ancestors deleted.
[STOP] [2021-04-19 15:16:25] build_node_ancestors
[WARN] [2021-04-19 15:16:25] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:16:25] Flattener#flatten
[STOP] [2021-04-19 15:16:25] rebuild_nodes
[START] [2021-04-19 15:16:25] resolve_missing_media_owners
[STOP] [2021-04-19 15:16:25] resolve_missing_media_owners
[START] [2021-04-19 15:16:25] sanitize_media_verbatims
[STOP] [2021-04-19 15:16:25] sanitize_media_verbatims
[START] [2021-04-19 15:16:25] queue_downloads
[STOP] [2021-04-19 15:16:25] queue_downloads
[START] [2021-04-19 15:16:25] parse_names
[WARN] [2021-04-19 15:16:25] I see 3 names which still need to be parsed.
[STOP] [2021-04-19 15:16:26] parse_names
[START] [2021-04-19 15:16:26] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:16:26] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:16:26] match_nodes
[START] [2021-04-19 15:16:26] map_all_nodes_to_pages
[STOP] [2021-04-19 15:16:26] map_all_nodes_to_pages
[INFO] [2021-04-19 15:16:26] ZERO unmatched nodes (of 3)! Nicely done.
[START] [2021-04-19 15:16:26] update_nodes
[STOP] [2021-04-19 15:16:26] update_nodes
[STOP] [2021-04-19 15:16:26] match_nodes
[START] [2021-04-19 15:16:26] reindex_search
[STOP] [2021-04-19 15:16:26] reindex_search
[START] [2021-04-19 15:16:26] normalize_units
[STOP] [2021-04-19 15:16:26] normalize_units
[START] [2021-04-19 15:16:26] calculate_statistics
[2021-04-19 15:16:26] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:16:26] calculate_statistics
[START] [2021-04-19 15:16:26] complete_harvest_instance
[START] [2021-04-19 15:16:26] overall_tsv_creation
[INFO] [2021-04-19 15:16:26] Processing group of 3 in 1 batches of 10000
[INFO] [2021-04-19 15:17:01] 3 Traits (unfiltered)...
[INFO] [2021-04-19 15:17:35] 3 Traits (filtered)...
[INFO] [2021-04-19 15:17:35] 0 Associations (filtered)...
[INFO] [2021-04-19 15:17:35] 3 metadata added.
[INFO] [2021-04-19 15:17:35] 0 metadata added.
[INFO] [2021-04-19 15:18:01] Average Time: 71.28
[INFO] [2021-04-19 15:18:01] Total Time: 1m36s
[STOP] [2021-04-19 15:18:01] overall_tsv_creation
[INFO] [2021-04-19 15:18:01] Done. Check your files:
[INFO] [2021-04-19 15:18:01] (3 lines) /app/public/data/elofsson_elofsso/publish_nodes.tsv
[INFO] [2021-04-19 15:18:01] (3 lines) /app/public/data/elofsson_elofsso/publish_scientific_names.tsv
[INFO] [2021-04-19 15:18:01] (4 lines) /app/public/data/elofsson_elofsso/publish_traits.tsv
[INFO] [2021-04-19 15:18:01] (4 lines) /app/public/data/elofsson_elofsso/publish_metadata.tsv
[STOP] [2021-04-19 15:18:01] complete_harvest_instance
[START] [2021-04-19 15:18:01] completed
[STOP] [2021-04-19 15:18:01] completed
[STOP] [2021-04-19 15:18:01] logged process, took 102.85

Latest Process

19 Apr 15:16 EXITED currently processing 0