Harvest for Picciani et al 2018 Created 19 Apr 09:51

Harvesting Log

# Logfile created on 2020-08-27 15:37:03 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:37:03] logged process
[START] [2020-08-27 15:37:03] Creating resource from OpenData
[START] [2020-08-27 15:37:04] logged process
[START] [2020-08-27 15:37:04] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:37:04] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:37:04] Creating resource from OpenData
[INFO] [2020-11-19 13:59:42] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 13:59:47] ## remove_type: ScientificName
[INFO] [2020-11-19 13:59:47] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:59:47] [13:59:47.445] Removed 0 Scientificnames
[INFO] [2020-11-19 13:59:47] ## remove_type: Vernacular
[INFO] [2020-11-19 13:59:47] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:59:47] [13:59:47.447] Removed 0 Vernaculars
[INFO] [2020-11-19 13:59:47] ## remove_type: Article
[INFO] [2020-11-19 13:59:47] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:59:47] [13:59:47.450] Removed 0 Articles
[INFO] [2020-11-19 13:59:47] ## remove_type: Medium
[INFO] [2020-11-19 13:59:47] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:59:47] [13:59:47.453] Removed 0 Media
[INFO] [2020-11-19 13:59:47] ## remove_type: Trait
[INFO] [2020-11-19 13:59:47] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:59:47] [13:59:47.456] Removed 0 Traits
[INFO] [2020-11-19 13:59:47] ## remove_type: MetaTrait
[INFO] [2020-11-19 13:59:47] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:59:47] [13:59:47.459] Removed 0 Metatraits
[INFO] [2020-11-19 13:59:47] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 13:59:47] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:59:47] [13:59:47.461] Removed 0 Occurrencemetadata
[INFO] [2020-11-19 13:59:47] ## remove_type: Assoc
[INFO] [2020-11-19 13:59:47] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:59:47] [13:59:47.464] Removed 0 Assocs
[INFO] [2020-11-19 13:59:47] ## remove_type: MetaAssoc
[INFO] [2020-11-19 13:59:47] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:59:47] [13:59:47.467] Removed 0 Metaassocs
[INFO] [2020-11-19 13:59:47] ## remove_type: Identifier
[INFO] [2020-11-19 13:59:47] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:59:47] [13:59:47.469] Removed 0 Identifiers
[INFO] [2020-11-19 13:59:47] ## remove_type: Reference
[INFO] [2020-11-19 13:59:47] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:59:47] [13:59:47.471] Removed 0 References
[INFO] [2020-11-19 13:59:47] ## remove_type: Node
[INFO] [2020-11-19 13:59:47] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:59:47] [13:59:47.514] Removed 0 Nodes
[START] [2020-11-19 13:59:47] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:59:47] Creating resource from OpenData
[START] [2020-11-19 13:59:47] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:59:47] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:59:47] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:59:47] Creating resource from OpenData
[START] [2020-11-19 13:59:47] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:59:47] create_harvest_instance
[STOP] [2020-11-19 13:59:49] create_harvest_instance
[START] [2020-11-19 13:59:49] fetch_files
[STOP] [2020-11-19 13:59:49] fetch_files
[START] [2020-11-19 13:59:49] validate_each_file
[STOP] [2020-11-19 13:59:49] validate_each_file
[START] [2020-11-19 13:59:49] convert_to_csv
[CMD] [2020-11-19 13:59:49] /usr/bin/sort /app/public/converted_csv/picciani_et_al_p_refs_24502.csv > /app/public/converted_csv/picciani_et_al_p_refs_24502.csv_sorted
[CMD] [2020-11-19 13:59:49] /usr/bin/sort /app/public/converted_csv/picciani_et_al_p_nodes_24503.csv > /app/public/converted_csv/picciani_et_al_p_nodes_24503.csv_sorted
[CMD] [2020-11-19 13:59:49] /usr/bin/sort /app/public/converted_csv/picciani_et_al_p_occurrences_24504.csv > /app/public/converted_csv/picciani_et_al_p_occurrences_24504.csv_sorted
[CMD] [2020-11-19 13:59:49] /usr/bin/sort /app/public/converted_csv/picciani_et_al_p_measurements_24505.csv > /app/public/converted_csv/picciani_et_al_p_measurements_24505.csv_sorted
[STOP] [2020-11-19 13:59:49] convert_to_csv
[START] [2020-11-19 13:59:49] calculate_delta
[CMD] [2020-11-19 13:59:49] echo "0a" > /app/public/diff/picciani_et_al_p_refs_24502.diff
[CMD] [2020-11-19 13:59:49] tail -n +1 /app/public/converted_csv/picciani_et_al_p_refs_24502.csv >> /app/public/diff/picciani_et_al_p_refs_24502.diff
[CMD] [2020-11-19 13:59:49] echo "." >> /app/public/diff/picciani_et_al_p_refs_24502.diff
[CMD] [2020-11-19 13:59:49] echo "0a" > /app/public/diff/picciani_et_al_p_nodes_24503.diff
[CMD] [2020-11-19 13:59:49] tail -n +1 /app/public/converted_csv/picciani_et_al_p_nodes_24503.csv >> /app/public/diff/picciani_et_al_p_nodes_24503.diff
[CMD] [2020-11-19 13:59:49] echo "." >> /app/public/diff/picciani_et_al_p_nodes_24503.diff
[CMD] [2020-11-19 13:59:49] echo "0a" > /app/public/diff/picciani_et_al_p_occurrences_24504.diff
[CMD] [2020-11-19 13:59:49] tail -n +1 /app/public/converted_csv/picciani_et_al_p_occurrences_24504.csv >> /app/public/diff/picciani_et_al_p_occurrences_24504.diff
[CMD] [2020-11-19 13:59:49] echo "." >> /app/public/diff/picciani_et_al_p_occurrences_24504.diff
[CMD] [2020-11-19 13:59:49] echo "0a" > /app/public/diff/picciani_et_al_p_measurements_24505.diff
[CMD] [2020-11-19 13:59:49] tail -n +1 /app/public/converted_csv/picciani_et_al_p_measurements_24505.csv >> /app/public/diff/picciani_et_al_p_measurements_24505.diff
[CMD] [2020-11-19 13:59:49] echo "." >> /app/public/diff/picciani_et_al_p_measurements_24505.diff
[STOP] [2020-11-19 13:59:49] calculate_delta
[START] [2020-11-19 13:59:49] parse_diff_and_store
[INFO] [2020-11-19 13:59:49] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 13:59:49] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 13:59:49] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 13:59:49] Loading measurements diff file into memory (true lines)...
[WARN] [2020-11-19 13:59:50] IGNORING a measurement NOT of a taxon (35a) with NO parent and NO occurrence ID.
[INFO] [2020-11-19 13:59:50] Storing 20 ScientificNames
[INFO] [2020-11-19 13:59:50] Processing group of 20 in 1 groups of 1000
[INFO] [2020-11-19 13:59:50] Average Time: 0.03
[INFO] [2020-11-19 13:59:50] Total Time: 1s
[INFO] [2020-11-19 13:59:50] Storing 20 Nodes
[INFO] [2020-11-19 13:59:50] Processing group of 20 in 1 groups of 1000
[INFO] [2020-11-19 13:59:50] Average Time: 0.01
[INFO] [2020-11-19 13:59:50] Total Time: 1s
[INFO] [2020-11-19 13:59:50] Storing 20 Occurrences
[INFO] [2020-11-19 13:59:50] Processing group of 20 in 1 groups of 1000
[INFO] [2020-11-19 13:59:51] Average Time: 0.04
[INFO] [2020-11-19 13:59:51] Total Time: 1s
[INFO] [2020-11-19 13:59:51] Storing 61 Traits
[INFO] [2020-11-19 13:59:51] Processing group of 61 in 1 groups of 1000
[INFO] [2020-11-19 13:59:51] Average Time: 0.05
[INFO] [2020-11-19 13:59:51] Total Time: 1s
[INFO] [2020-11-19 13:59:51] Storing 33 MetaTraits
[INFO] [2020-11-19 13:59:51] Processing group of 33 in 1 groups of 1000
[INFO] [2020-11-19 13:59:51] Average Time: 0.01
[INFO] [2020-11-19 13:59:51] Total Time: 1s
[STOP] [2020-11-19 13:59:51] parse_diff_and_store
[START] [2020-11-19 13:59:51] resolve_keys
[INFO] [2020-11-19 13:59:56] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-19 13:59:56] traits to occurrences...
[INFO] [2020-11-19 13:59:56] traits to nodes (through occurrences)...
[INFO] [2020-11-19 13:59:56] Traits to sex term...
[INFO] [2020-11-19 13:59:56] Traits to lifestage term...
[INFO] [2020-11-19 13:59:56] MetaTraits to traits...
[INFO] [2020-11-19 13:59:56] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-19 13:59:56] Assocs to occurrences...
[INFO] [2020-11-19 13:59:57] Assocs to nodes...
[INFO] [2020-11-19 13:59:57] Assoc to sex term...
[INFO] [2020-11-19 13:59:57] Assoc to lifestage term...
[INFO] [2020-11-19 13:59:57] MetaAssoc to assocs...
[STOP] [2020-11-19 13:59:57] resolve_keys
[START] [2020-11-19 13:59:57] hold_for_later_1
[STOP] [2020-11-19 13:59:57] hold_for_later_1
[START] [2020-11-19 13:59:57] hold_for_later_2
[STOP] [2020-11-19 13:59:57] hold_for_later_2
[START] [2020-11-19 13:59:57] resolve_missing_parents
[STOP] [2020-11-19 13:59:57] resolve_missing_parents
[START] [2020-11-19 13:59:57] rebuild_nodes
[START] [2020-11-19 13:59:57] Flattener#flatten
[START] [2020-11-19 13:59:57] Flattener#study_resource
[START] [2020-11-19 13:59:57] Flattener#build_ancestry
[STOP] [2020-11-19 13:59:57] Flattener#build_ancestry
[INFO] [2020-11-19 13:59:57] 20 ancestry keys
[START] [2020-11-19 13:59:57] build_node_ancestors
[INFO] [2020-11-19 13:59:57] old ancestors deleted.
[STOP] [2020-11-19 13:59:57] build_node_ancestors
[WARN] [2020-11-19 13:59:57] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-19 13:59:57] Flattener#flatten
[STOP] [2020-11-19 13:59:57] rebuild_nodes
[START] [2020-11-19 13:59:57] resolve_missing_media_owners
[STOP] [2020-11-19 13:59:57] resolve_missing_media_owners
[START] [2020-11-19 13:59:57] sanitize_media_verbatims
[STOP] [2020-11-19 13:59:57] sanitize_media_verbatims
[START] [2020-11-19 13:59:57] queue_downloads
[STOP] [2020-11-19 13:59:57] queue_downloads
[START] [2020-11-19 13:59:57] parse_names
[WARN] [2020-11-19 13:59:57] I see 20 names which still need to be parsed.
[STOP] [2020-11-19 13:59:58] parse_names
[START] [2020-11-19 13:59:58] denormalize_canonical_names_to_nodes
[STOP] [2020-11-19 13:59:58] denormalize_canonical_names_to_nodes
[START] [2020-11-19 13:59:58] match_nodes
[START] [2020-11-19 13:59:58] map_all_nodes_to_pages
[STOP] [2020-11-19 13:59:58] map_all_nodes_to_pages
[INFO] [2020-11-19 13:59:58] ZERO unmatched nodes (of 20)! Nicely done.
[START] [2020-11-19 13:59:58] update_nodes
[STOP] [2020-11-19 13:59:58] update_nodes
[STOP] [2020-11-19 13:59:58] match_nodes
[START] [2020-11-19 13:59:58] reindex_search
[STOP] [2020-11-19 13:59:58] reindex_search
[START] [2020-11-19 13:59:58] normalize_units
[STOP] [2020-11-19 13:59:58] normalize_units
[START] [2020-11-19 13:59:58] calculate_statistics
[2020-11-19 13:59:58] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-19 13:59:58] calculate_statistics
[START] [2020-11-19 13:59:58] complete_harvest_instance
[START] [2020-11-19 13:59:58] overall_tsv_creation
[INFO] [2020-11-19 13:59:58] Processing group of 20 in 1 batches of 10000
[INFO] [2020-11-19 14:00:42] 21 Traits (unfiltered)...
[INFO] [2020-11-19 14:01:27] 21 Traits (filtered)...
[INFO] [2020-11-19 14:01:27] 0 Associations (filtered)...
[INFO] [2020-11-19 14:01:27] 73 metadata added.
[INFO] [2020-11-19 14:01:27] 0 metadata added.
[INFO] [2020-11-19 14:01:27] Average Time: 69.28
[INFO] [2020-11-19 14:01:27] Total Time: 1m30s
[STOP] [2020-11-19 14:01:27] overall_tsv_creation
[INFO] [2020-11-19 14:01:27] Done. Check your files:
[INFO] [2020-11-19 14:01:27] (20 lines) /app/public/data/picciani_et_al_p/publish_nodes.tsv
[INFO] [2020-11-19 14:01:27] (20 lines) /app/public/data/picciani_et_al_p/publish_scientific_names.tsv
[INFO] [2020-11-19 14:01:27] (22 lines) /app/public/data/picciani_et_al_p/publish_traits.tsv
[INFO] [2020-11-19 14:01:27] (74 lines) /app/public/data/picciani_et_al_p/publish_metadata.tsv
[STOP] [2020-11-19 14:01:27] complete_harvest_instance
[START] [2020-11-19 14:01:27] completed
[STOP] [2020-11-19 14:01:27] completed
[STOP] [2020-11-19 14:01:27] logged process, took 99.58
[INFO] [2021-04-19 09:51:16] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 09:51:19] ## remove_type: ScientificName
[INFO] [2021-04-19 09:51:19] ++ Calling delete_all on 20 instances...
[INFO] [2021-04-19 09:51:19] [09:51:19.709] Removed 20 Scientificnames
[INFO] [2021-04-19 09:51:19] ## remove_type: Vernacular
[INFO] [2021-04-19 09:51:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:51:19] [09:51:19.711] Removed 0 Vernaculars
[INFO] [2021-04-19 09:51:19] ## remove_type: Article
[INFO] [2021-04-19 09:51:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:51:19] [09:51:19.712] Removed 0 Articles
[INFO] [2021-04-19 09:51:19] ## remove_type: Medium
[INFO] [2021-04-19 09:51:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:51:19] [09:51:19.713] Removed 0 Media
[INFO] [2021-04-19 09:51:19] ## remove_type: Trait
[INFO] [2021-04-19 09:51:19] ++ Calling delete_all on 61 instances...
[INFO] [2021-04-19 09:51:19] [09:51:19.716] Removed 61 Traits
[INFO] [2021-04-19 09:51:19] ## remove_type: MetaTrait
[INFO] [2021-04-19 09:51:19] ++ Calling delete_all on 33 instances...
[INFO] [2021-04-19 09:51:19] [09:51:19.719] Removed 33 Metatraits
[INFO] [2021-04-19 09:51:19] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 09:51:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:51:19] [09:51:19.720] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 09:51:19] ## remove_type: Assoc
[INFO] [2021-04-19 09:51:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:51:19] [09:51:19.721] Removed 0 Assocs
[INFO] [2021-04-19 09:51:19] ## remove_type: MetaAssoc
[INFO] [2021-04-19 09:51:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:51:19] [09:51:19.723] Removed 0 Metaassocs
[INFO] [2021-04-19 09:51:19] ## remove_type: Identifier
[INFO] [2021-04-19 09:51:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:51:19] [09:51:19.724] Removed 0 Identifiers
[INFO] [2021-04-19 09:51:19] ## remove_type: Reference
[INFO] [2021-04-19 09:51:19] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:51:19] [09:51:19.726] Removed 0 References
[INFO] [2021-04-19 09:51:19] Starting batch with ID 84620909...
[INFO] [2021-04-19 09:51:19] Starting batch with ID 84620909...
[INFO] [2021-04-19 09:51:19] Starting batch with ID 84620909...
[INFO] [2021-04-19 09:51:19] Starting batch with ID 84620909...
[INFO] [2021-04-19 09:51:19] Starting batch with ID 84620909...
[INFO] [2021-04-19 09:51:19] Starting batch with ID 84620909...
[INFO] [2021-04-19 09:51:19] Starting batch with ID 84620909...
[INFO] [2021-04-19 09:51:19] Starting batch with ID 84620909...
[INFO] [2021-04-19 09:51:19] Starting batch with ID 84620909...
[INFO] [2021-04-19 09:51:19] Starting batch with ID 84620909...
[INFO] [2021-04-19 09:51:19] Starting batch with ID 84620906...
[INFO] [2021-04-19 09:51:19] ## remove_type: Node
[INFO] [2021-04-19 09:51:19] ++ Calling delete_all on 20 instances...
[INFO] [2021-04-19 09:51:19] [09:51:19.839] Removed 20 Nodes
[START] [2021-04-19 09:51:20] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 09:51:20] Creating resource from OpenData
[START] [2021-04-19 09:51:21] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 09:51:21] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 09:51:26] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 09:51:26] Creating resource from OpenData
[START] [2021-04-19 09:51:26] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 09:51:26] create_harvest_instance
[INFO] [2021-04-19 09:51:26] Created harvest instance #3721
[STOP] [2021-04-19 09:51:26] create_harvest_instance
[START] [2021-04-19 09:51:26] fetch_files
[STOP] [2021-04-19 09:51:26] fetch_files
[START] [2021-04-19 09:51:26] validate_each_file
[INFO] [2021-04-19 09:51:26] Looping over 4 formats...
[INFO] [2021-04-19 09:51:26] ...refs (/app/public/data/picciani_et_al_p/references.tsv)
[INFO] [2021-04-19 09:51:26] Valid: /app/public/converted_csv/picciani_et_al_p_refs_3721.csv (0 lines)
[INFO] [2021-04-19 09:51:26] ...nodes (/app/public/data/picciani_et_al_p/taxa.txt)
[INFO] [2021-04-19 09:51:26] Valid: /app/public/converted_csv/picciani_et_al_p_nodes_3721.csv (20 lines)
[INFO] [2021-04-19 09:51:26] ...occurrences (/app/public/data/picciani_et_al_p/occurrences.txt)
[INFO] [2021-04-19 09:51:26] Valid: /app/public/converted_csv/picciani_et_al_p_occurrences_3721.csv (20 lines)
[INFO] [2021-04-19 09:51:26] ...measurements (/app/public/data/picciani_et_al_p/measurementsorfacts.txt)
[INFO] [2021-04-19 09:51:26] Valid: /app/public/converted_csv/picciani_et_al_p_measurements_3721.csv (62 lines)
[STOP] [2021-04-19 09:51:26] validate_each_file
[START] [2021-04-19 09:51:26] convert_to_csv
[INFO] [2021-04-19 09:51:26] Looping over 4 formats...
[INFO] [2021-04-19 09:51:26] ...refs (/app/public/data/picciani_et_al_p/references.tsv)
[CMD] [2021-04-19 09:51:26] /usr/bin/sort /app/public/converted_csv/picciani_et_al_p_refs_3721.csv > /app/public/converted_csv/picciani_et_al_p_refs_3721.csv_sorted
[INFO] [2021-04-19 09:51:27] Converted: /app/public/converted_csv/picciani_et_al_p_refs_3721.csv (0 lines)
[INFO] [2021-04-19 09:51:27] ...nodes (/app/public/data/picciani_et_al_p/taxa.txt)
[CMD] [2021-04-19 09:51:27] /usr/bin/sort /app/public/converted_csv/picciani_et_al_p_nodes_3721.csv > /app/public/converted_csv/picciani_et_al_p_nodes_3721.csv_sorted
[INFO] [2021-04-19 09:51:27] Converted: /app/public/converted_csv/picciani_et_al_p_nodes_3721.csv (20 lines)
[INFO] [2021-04-19 09:51:27] ...occurrences (/app/public/data/picciani_et_al_p/occurrences.txt)
[CMD] [2021-04-19 09:51:27] /usr/bin/sort /app/public/converted_csv/picciani_et_al_p_occurrences_3721.csv > /app/public/converted_csv/picciani_et_al_p_occurrences_3721.csv_sorted
[INFO] [2021-04-19 09:51:28] Converted: /app/public/converted_csv/picciani_et_al_p_occurrences_3721.csv (20 lines)
[INFO] [2021-04-19 09:51:28] ...measurements (/app/public/data/picciani_et_al_p/measurementsorfacts.txt)
[CMD] [2021-04-19 09:51:28] /usr/bin/sort /app/public/converted_csv/picciani_et_al_p_measurements_3721.csv > /app/public/converted_csv/picciani_et_al_p_measurements_3721.csv_sorted
[INFO] [2021-04-19 09:51:28] Converted: /app/public/converted_csv/picciani_et_al_p_measurements_3721.csv (62 lines)
[STOP] [2021-04-19 09:51:28] convert_to_csv
[START] [2021-04-19 09:51:28] calculate_delta
[INFO] [2021-04-19 09:51:28] Looping over 4 formats...
[INFO] [2021-04-19 09:51:28] ...refs (/app/public/data/picciani_et_al_p/references.tsv)
[CMD] [2021-04-19 09:51:28] echo "0a" > /app/public/diff/picciani_et_al_p_refs_3721.diff
[CMD] [2021-04-19 09:51:28] tail -n +1 /app/public/converted_csv/picciani_et_al_p_refs_3721.csv >> /app/public/diff/picciani_et_al_p_refs_3721.diff
[CMD] [2021-04-19 09:51:29] echo "." >> /app/public/diff/picciani_et_al_p_refs_3721.diff
[INFO] [2021-04-19 09:51:29] Created diff: /app/public/diff/picciani_et_al_p_refs_3721.diff (2 lines)
[INFO] [2021-04-19 09:51:29] ...nodes (/app/public/data/picciani_et_al_p/taxa.txt)
[CMD] [2021-04-19 09:51:29] echo "0a" > /app/public/diff/picciani_et_al_p_nodes_3721.diff
[CMD] [2021-04-19 09:51:29] tail -n +1 /app/public/converted_csv/picciani_et_al_p_nodes_3721.csv >> /app/public/diff/picciani_et_al_p_nodes_3721.diff
[CMD] [2021-04-19 09:51:30] echo "." >> /app/public/diff/picciani_et_al_p_nodes_3721.diff
[INFO] [2021-04-19 09:51:30] Created diff: /app/public/diff/picciani_et_al_p_nodes_3721.diff (22 lines)
[INFO] [2021-04-19 09:51:30] ...occurrences (/app/public/data/picciani_et_al_p/occurrences.txt)
[CMD] [2021-04-19 09:51:30] echo "0a" > /app/public/diff/picciani_et_al_p_occurrences_3721.diff
[CMD] [2021-04-19 09:51:31] tail -n +1 /app/public/converted_csv/picciani_et_al_p_occurrences_3721.csv >> /app/public/diff/picciani_et_al_p_occurrences_3721.diff
[CMD] [2021-04-19 09:51:31] echo "." >> /app/public/diff/picciani_et_al_p_occurrences_3721.diff
[INFO] [2021-04-19 09:51:31] Created diff: /app/public/diff/picciani_et_al_p_occurrences_3721.diff (22 lines)
[INFO] [2021-04-19 09:51:31] ...measurements (/app/public/data/picciani_et_al_p/measurementsorfacts.txt)
[CMD] [2021-04-19 09:51:31] echo "0a" > /app/public/diff/picciani_et_al_p_measurements_3721.diff
[CMD] [2021-04-19 09:51:32] tail -n +1 /app/public/converted_csv/picciani_et_al_p_measurements_3721.csv >> /app/public/diff/picciani_et_al_p_measurements_3721.diff
[CMD] [2021-04-19 09:51:32] echo "." >> /app/public/diff/picciani_et_al_p_measurements_3721.diff
[INFO] [2021-04-19 09:51:33] Created diff: /app/public/diff/picciani_et_al_p_measurements_3721.diff (64 lines)
[STOP] [2021-04-19 09:51:33] calculate_delta
[START] [2021-04-19 09:51:33] parse_diff_and_store
[INFO] [2021-04-19 09:51:33] Handling diff: /app/public/diff/picciani_et_al_p_refs_3721.diff (2 lines)
[INFO] [2021-04-19 09:51:33] Loading refs diff file into memory (2 /app/public/diff/picciani_et_al_p_refs_3721.diff lines)...
[INFO] [2021-04-19 09:51:33] Handling diff: /app/public/diff/picciani_et_al_p_nodes_3721.diff (22 lines)
[INFO] [2021-04-19 09:51:34] Loading nodes diff file into memory (22 /app/public/diff/picciani_et_al_p_nodes_3721.diff lines)...
[INFO] [2021-04-19 09:51:34] Handling diff: /app/public/diff/picciani_et_al_p_occurrences_3721.diff (22 lines)
[INFO] [2021-04-19 09:51:35] Loading occurrences diff file into memory (22 /app/public/diff/picciani_et_al_p_occurrences_3721.diff lines)...
[INFO] [2021-04-19 09:51:35] Handling diff: /app/public/diff/picciani_et_al_p_measurements_3721.diff (64 lines)
[INFO] [2021-04-19 09:51:35] Loading measurements diff file into memory (64 /app/public/diff/picciani_et_al_p_measurements_3721.diff lines)...
[WARN] [2021-04-19 09:51:36] IGNORING a measurement NOT of a taxon (35a) with NO parent and NO occurrence ID.
[INFO] [2021-04-19 09:51:36] Storing 20 ScientificNames
[INFO] [2021-04-19 09:51:36] Processing group of 20 in 1 groups of 1000
[INFO] [2021-04-19 09:51:36] Average Time: 0.01
[INFO] [2021-04-19 09:51:36] Total Time: 1s
[INFO] [2021-04-19 09:51:36] Storing 20 Nodes
[INFO] [2021-04-19 09:51:36] Processing group of 20 in 1 groups of 1000
[INFO] [2021-04-19 09:51:36] Average Time: 0.01
[INFO] [2021-04-19 09:51:36] Total Time: 1s
[INFO] [2021-04-19 09:51:36] Storing 20 Occurrences
[INFO] [2021-04-19 09:51:36] Processing group of 20 in 1 groups of 1000
[INFO] [2021-04-19 09:51:36] Average Time: 0.0
[INFO] [2021-04-19 09:51:36] Total Time: 1s
[INFO] [2021-04-19 09:51:36] Storing 61 Traits
[INFO] [2021-04-19 09:51:36] Processing group of 61 in 1 groups of 1000
[INFO] [2021-04-19 09:51:36] Average Time: 0.03
[INFO] [2021-04-19 09:51:36] Total Time: 1s
[INFO] [2021-04-19 09:51:36] Storing 33 MetaTraits
[INFO] [2021-04-19 09:51:36] Processing group of 33 in 1 groups of 1000
[INFO] [2021-04-19 09:51:36] Average Time: 0.01
[INFO] [2021-04-19 09:51:36] Total Time: 1s
[STOP] [2021-04-19 09:51:36] parse_diff_and_store
[START] [2021-04-19 09:51:36] resolve_keys
[INFO] [2021-04-19 09:51:42] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 09:51:42] traits to occurrences...
[INFO] [2021-04-19 09:51:42] traits to nodes (through occurrences)...
[INFO] [2021-04-19 09:51:42] Traits to sex term...
[INFO] [2021-04-19 09:51:42] Traits to lifestage term...
[INFO] [2021-04-19 09:51:42] MetaTraits to traits...
[INFO] [2021-04-19 09:51:42] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 09:51:42] Assocs to occurrences...
[INFO] [2021-04-19 09:51:42] Assocs to nodes...
[INFO] [2021-04-19 09:51:42] Assoc to sex term...
[INFO] [2021-04-19 09:51:42] Assoc to lifestage term...
[INFO] [2021-04-19 09:51:42] MetaAssoc to assocs...
[STOP] [2021-04-19 09:51:42] resolve_keys
[START] [2021-04-19 09:51:42] hold_for_later_1
[STOP] [2021-04-19 09:51:42] hold_for_later_1
[START] [2021-04-19 09:51:42] hold_for_later_2
[STOP] [2021-04-19 09:51:42] hold_for_later_2
[START] [2021-04-19 09:51:42] resolve_missing_parents
[STOP] [2021-04-19 09:51:42] resolve_missing_parents
[START] [2021-04-19 09:51:42] rebuild_nodes
[START] [2021-04-19 09:51:42] Flattener#flatten
[START] [2021-04-19 09:51:42] Flattener#study_resource
[START] [2021-04-19 09:51:42] Flattener#build_ancestry
[STOP] [2021-04-19 09:51:42] Flattener#build_ancestry
[INFO] [2021-04-19 09:51:42] 20 ancestry keys
[START] [2021-04-19 09:51:42] build_node_ancestors
[INFO] [2021-04-19 09:51:42] old ancestors deleted.
[STOP] [2021-04-19 09:51:42] build_node_ancestors
[WARN] [2021-04-19 09:51:42] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 09:51:42] Flattener#flatten
[STOP] [2021-04-19 09:51:42] rebuild_nodes
[START] [2021-04-19 09:51:42] resolve_missing_media_owners
[STOP] [2021-04-19 09:51:42] resolve_missing_media_owners
[START] [2021-04-19 09:51:42] sanitize_media_verbatims
[STOP] [2021-04-19 09:51:42] sanitize_media_verbatims
[START] [2021-04-19 09:51:42] queue_downloads
[STOP] [2021-04-19 09:51:42] queue_downloads
[START] [2021-04-19 09:51:42] parse_names
[WARN] [2021-04-19 09:51:42] I see 20 names which still need to be parsed.
[STOP] [2021-04-19 09:51:43] parse_names
[START] [2021-04-19 09:51:43] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 09:51:43] denormalize_canonical_names_to_nodes
[START] [2021-04-19 09:51:43] match_nodes
[START] [2021-04-19 09:51:43] map_all_nodes_to_pages
[STOP] [2021-04-19 09:51:43] map_all_nodes_to_pages
[INFO] [2021-04-19 09:51:43] ZERO unmatched nodes (of 20)! Nicely done.
[START] [2021-04-19 09:51:43] update_nodes
[STOP] [2021-04-19 09:51:43] update_nodes
[STOP] [2021-04-19 09:51:43] match_nodes
[START] [2021-04-19 09:51:43] reindex_search
[STOP] [2021-04-19 09:51:43] reindex_search
[START] [2021-04-19 09:51:43] normalize_units
[STOP] [2021-04-19 09:51:43] normalize_units
[START] [2021-04-19 09:51:43] calculate_statistics
[2021-04-19 09:51:43] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 09:51:43] calculate_statistics
[START] [2021-04-19 09:51:43] complete_harvest_instance
[START] [2021-04-19 09:51:43] overall_tsv_creation
[INFO] [2021-04-19 09:51:43] Processing group of 20 in 1 batches of 10000
[INFO] [2021-04-19 09:52:20] 21 Traits (unfiltered)...
[INFO] [2021-04-19 09:52:54] 21 Traits (filtered)...
[INFO] [2021-04-19 09:52:54] 0 Associations (filtered)...
[INFO] [2021-04-19 09:52:54] 40 metadata added.
[INFO] [2021-04-19 09:52:54] 0 metadata added.
[INFO] [2021-04-19 09:53:21] Average Time: 73.6
[INFO] [2021-04-19 09:53:21] Total Time: 1m38s
[STOP] [2021-04-19 09:53:21] overall_tsv_creation
[INFO] [2021-04-19 09:53:21] Done. Check your files:
[INFO] [2021-04-19 09:53:22] (20 lines) /app/public/data/picciani_et_al_p/publish_nodes.tsv
[INFO] [2021-04-19 09:53:22] (20 lines) /app/public/data/picciani_et_al_p/publish_scientific_names.tsv
[INFO] [2021-04-19 09:53:22] (22 lines) /app/public/data/picciani_et_al_p/publish_traits.tsv
[INFO] [2021-04-19 09:53:23] (41 lines) /app/public/data/picciani_et_al_p/publish_metadata.tsv
[STOP] [2021-04-19 09:53:23] complete_harvest_instance
[START] [2021-04-19 09:53:23] completed
[STOP] [2021-04-19 09:53:23] completed
[STOP] [2021-04-19 09:53:23] logged process, took 117.37

Latest Process

19 Apr 09:51 EXITED currently processing 0