Harvest for Warrant et al 2003 Created 19 Apr 15:45

Stage: completed
Fetched: 19 Apr 15:45
Validated: 19 Apr 15:45
Deltas Created 19 Apr 15:45
Units Normalized: 19 Apr 15:46
Ancestry Built: 19 Apr 15:45
Nodes Matched: 19 Apr 15:46
Names Parsed: 19 Apr 15:46
New Models Stored: 19 Apr 15:45
Indexed: 19 Apr 15:46
Completed: 19 Apr 15:47
Time to Harvest: less than a minute

Harvesting Log (most recent first)

# Logfile created on 2020-08-27 15:45:45 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:45:45] logged process
[START] [2020-08-27 15:45:45] Creating resource from OpenData
[START] [2020-08-27 15:45:45] logged process
[START] [2020-08-27 15:45:45] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:45:46] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:45:46] Creating resource from OpenData
[INFO] [2020-12-03 11:46:15] ## HARVEST: type = -harvest
[START] [2020-12-03 11:46:20] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-12-03 11:46:20] create_harvest_instance
[STOP] [2020-12-03 11:46:21] create_harvest_instance
[START] [2020-12-03 11:46:21] fetch_files
[STOP] [2020-12-03 11:46:21] fetch_files
[START] [2020-12-03 11:46:21] validate_each_file
[STOP] [2020-12-03 11:46:21] validate_each_file
[START] [2020-12-03 11:46:21] convert_to_csv
[CMD] [2020-12-03 11:46:21] /usr/bin/sort /app/public/converted_csv/warrant_et_al_wa_refs_24840.csv > /app/public/converted_csv/warrant_et_al_wa_refs_24840.csv_sorted
[CMD] [2020-12-03 11:46:21] /usr/bin/sort /app/public/converted_csv/warrant_et_al_wa_nodes_24841.csv > /app/public/converted_csv/warrant_et_al_wa_nodes_24841.csv_sorted
[CMD] [2020-12-03 11:46:21] /usr/bin/sort /app/public/converted_csv/warrant_et_al_wa_occurrences_24842.csv > /app/public/converted_csv/warrant_et_al_wa_occurrences_24842.csv_sorted
[CMD] [2020-12-03 11:46:21] /usr/bin/sort /app/public/converted_csv/warrant_et_al_wa_measurements_24843.csv > /app/public/converted_csv/warrant_et_al_wa_measurements_24843.csv_sorted
[STOP] [2020-12-03 11:46:21] convert_to_csv
[START] [2020-12-03 11:46:21] calculate_delta
[CMD] [2020-12-03 11:46:21] echo "0a" > /app/public/diff/warrant_et_al_wa_refs_24840.diff
[CMD] [2020-12-03 11:46:21] tail -n +1 /app/public/converted_csv/warrant_et_al_wa_refs_24840.csv >> /app/public/diff/warrant_et_al_wa_refs_24840.diff
[CMD] [2020-12-03 11:46:21] echo "." >> /app/public/diff/warrant_et_al_wa_refs_24840.diff
[CMD] [2020-12-03 11:46:21] echo "0a" > /app/public/diff/warrant_et_al_wa_nodes_24841.diff
[CMD] [2020-12-03 11:46:21] tail -n +1 /app/public/converted_csv/warrant_et_al_wa_nodes_24841.csv >> /app/public/diff/warrant_et_al_wa_nodes_24841.diff
[CMD] [2020-12-03 11:46:21] echo "." >> /app/public/diff/warrant_et_al_wa_nodes_24841.diff
[CMD] [2020-12-03 11:46:21] echo "0a" > /app/public/diff/warrant_et_al_wa_occurrences_24842.diff
[CMD] [2020-12-03 11:46:21] tail -n +1 /app/public/converted_csv/warrant_et_al_wa_occurrences_24842.csv >> /app/public/diff/warrant_et_al_wa_occurrences_24842.diff
[CMD] [2020-12-03 11:46:21] echo "." >> /app/public/diff/warrant_et_al_wa_occurrences_24842.diff
[CMD] [2020-12-03 11:46:21] echo "0a" > /app/public/diff/warrant_et_al_wa_measurements_24843.diff
[CMD] [2020-12-03 11:46:21] tail -n +1 /app/public/converted_csv/warrant_et_al_wa_measurements_24843.csv >> /app/public/diff/warrant_et_al_wa_measurements_24843.diff
[CMD] [2020-12-03 11:46:21] echo "." >> /app/public/diff/warrant_et_al_wa_measurements_24843.diff
[STOP] [2020-12-03 11:46:21] calculate_delta
[START] [2020-12-03 11:46:21] parse_diff_and_store
[INFO] [2020-12-03 11:46:21] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 11:46:21] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 11:46:21] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 11:46:21] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 11:46:22] Storing 10 ScientificNames
[INFO] [2020-12-03 11:46:22] Processing group of 10 in 1 groups of 1000
[INFO] [2020-12-03 11:46:22] Average Time: 0.03
[INFO] [2020-12-03 11:46:22] Total Time: 1s
[INFO] [2020-12-03 11:46:22] Storing 10 Nodes
[INFO] [2020-12-03 11:46:22] Processing group of 10 in 1 groups of 1000
[INFO] [2020-12-03 11:46:22] Average Time: 0.0
[INFO] [2020-12-03 11:46:22] Total Time: 1s
[INFO] [2020-12-03 11:46:22] Storing 10 Occurrences
[INFO] [2020-12-03 11:46:22] Processing group of 10 in 1 groups of 1000
[INFO] [2020-12-03 11:46:22] Average Time: 0.0
[INFO] [2020-12-03 11:46:22] Total Time: 1s
[INFO] [2020-12-03 11:46:22] Storing 30 Traits
[INFO] [2020-12-03 11:46:22] Processing group of 30 in 1 groups of 1000
[INFO] [2020-12-03 11:46:22] Average Time: 0.02
[INFO] [2020-12-03 11:46:22] Total Time: 1s
[INFO] [2020-12-03 11:46:22] Storing 10 MetaTraits
[INFO] [2020-12-03 11:46:22] Processing group of 10 in 1 groups of 1000
[INFO] [2020-12-03 11:46:22] Average Time: 0.0
[INFO] [2020-12-03 11:46:22] Total Time: 1s
[STOP] [2020-12-03 11:46:22] parse_diff_and_store
[START] [2020-12-03 11:46:22] resolve_keys
[INFO] [2020-12-03 11:46:28] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 11:46:28] traits to occurrences...
[INFO] [2020-12-03 11:46:28] traits to nodes (through occurrences)...
[INFO] [2020-12-03 11:46:28] Traits to sex term...
[INFO] [2020-12-03 11:46:28] Traits to lifestage term...
[INFO] [2020-12-03 11:46:28] MetaTraits to traits...
[INFO] [2020-12-03 11:46:28] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 11:46:28] Assocs to occurrences...
[INFO] [2020-12-03 11:46:28] Assocs to nodes...
[INFO] [2020-12-03 11:46:28] Assoc to sex term...
[INFO] [2020-12-03 11:46:28] Assoc to lifestage term...
[INFO] [2020-12-03 11:46:28] MetaAssoc to assocs...
[STOP] [2020-12-03 11:46:28] resolve_keys
[START] [2020-12-03 11:46:28] hold_for_later_1
[STOP] [2020-12-03 11:46:28] hold_for_later_1
[START] [2020-12-03 11:46:28] hold_for_later_2
[STOP] [2020-12-03 11:46:28] hold_for_later_2
[START] [2020-12-03 11:46:28] resolve_missing_parents
[STOP] [2020-12-03 11:46:28] resolve_missing_parents
[START] [2020-12-03 11:46:28] rebuild_nodes
[START] [2020-12-03 11:46:28] Flattener#flatten
[START] [2020-12-03 11:46:28] Flattener#study_resource
[START] [2020-12-03 11:46:28] Flattener#build_ancestry
[STOP] [2020-12-03 11:46:28] Flattener#build_ancestry
[INFO] [2020-12-03 11:46:28] 10 ancestry keys
[START] [2020-12-03 11:46:28] build_node_ancestors
[INFO] [2020-12-03 11:46:28] old ancestors deleted.
[STOP] [2020-12-03 11:46:28] build_node_ancestors
[WARN] [2020-12-03 11:46:28] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 11:46:28] Flattener#flatten
[STOP] [2020-12-03 11:46:28] rebuild_nodes
[START] [2020-12-03 11:46:28] resolve_missing_media_owners
[STOP] [2020-12-03 11:46:28] resolve_missing_media_owners
[START] [2020-12-03 11:46:28] sanitize_media_verbatims
[STOP] [2020-12-03 11:46:28] sanitize_media_verbatims
[START] [2020-12-03 11:46:28] queue_downloads
[STOP] [2020-12-03 11:46:28] queue_downloads
[START] [2020-12-03 11:46:28] parse_names
[WARN] [2020-12-03 11:46:28] I see 10 names which still need to be parsed.
[STOP] [2020-12-03 11:46:29] parse_names
[START] [2020-12-03 11:46:29] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 11:46:29] denormalize_canonical_names_to_nodes
[START] [2020-12-03 11:46:29] match_nodes
[START] [2020-12-03 11:46:29] map_all_nodes_to_pages
[STOP] [2020-12-03 11:46:29] map_all_nodes_to_pages
[INFO] [2020-12-03 11:46:29] ZERO unmatched nodes (of 10)! Nicely done.
[START] [2020-12-03 11:46:29] update_nodes
[STOP] [2020-12-03 11:46:29] update_nodes
[STOP] [2020-12-03 11:46:29] match_nodes
[START] [2020-12-03 11:46:29] reindex_search
[STOP] [2020-12-03 11:46:29] reindex_search
[START] [2020-12-03 11:46:29] normalize_units
[STOP] [2020-12-03 11:46:29] normalize_units
[START] [2020-12-03 11:46:30] calculate_statistics
[2020-12-03 11:46:30] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 11:46:30] calculate_statistics
[START] [2020-12-03 11:46:30] complete_harvest_instance
[START] [2020-12-03 11:46:30] overall_tsv_creation
[INFO] [2020-12-03 11:46:30] Processing group of 10 in 1 batches of 10000
[INFO] [2020-12-03 11:47:09] 10 Traits (unfiltered)...
[INFO] [2020-12-03 11:47:48] 10 Traits (filtered)...
[INFO] [2020-12-03 11:47:48] 0 Associations (filtered)...
[INFO] [2020-12-03 11:47:48] 30 metadata added.
[INFO] [2020-12-03 11:47:48] 0 metadata added.
[INFO] [2020-12-03 11:47:48] Average Time: 55.32
[INFO] [2020-12-03 11:47:48] Total Time: 1m19s
[STOP] [2020-12-03 11:47:48] overall_tsv_creation
[INFO] [2020-12-03 11:47:48] Done. Check your files:
[INFO] [2020-12-03 11:47:48] (10 lines) /app/public/data/warrant_et_al_wa/publish_nodes.tsv
[INFO] [2020-12-03 11:47:48] (10 lines) /app/public/data/warrant_et_al_wa/publish_scientific_names.tsv
[INFO] [2020-12-03 11:47:48] (11 lines) /app/public/data/warrant_et_al_wa/publish_traits.tsv
[INFO] [2020-12-03 11:47:48] (31 lines) /app/public/data/warrant_et_al_wa/publish_metadata.tsv
[STOP] [2020-12-03 11:47:48] complete_harvest_instance
[START] [2020-12-03 11:47:48] completed
[STOP] [2020-12-03 11:47:48] completed
[STOP] [2020-12-03 11:47:48] logged process, took 88.49
[INFO] [2021-04-19 10:08:50] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 10:08:51] ## remove_type: ScientificName
[INFO] [2021-04-19 10:08:51] ++ Calling delete_all on 10 instances...
[INFO] [2021-04-19 10:08:51] [10:08:51.177] Removed 10 Scientificnames
[INFO] [2021-04-19 10:08:51] ## remove_type: Vernacular
[INFO] [2021-04-19 10:08:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 10:08:51] [10:08:51.179] Removed 0 Vernaculars
[INFO] [2021-04-19 10:08:51] ## remove_type: Article
[INFO] [2021-04-19 10:08:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 10:08:51] [10:08:51.180] Removed 0 Articles
[INFO] [2021-04-19 10:08:51] ## remove_type: Medium
[INFO] [2021-04-19 10:08:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 10:08:51] [10:08:51.182] Removed 0 Media
[INFO] [2021-04-19 10:08:51] ## remove_type: Trait
[INFO] [2021-04-19 10:08:51] ++ Calling delete_all on 30 instances...
[INFO] [2021-04-19 10:08:51] [10:08:51.184] Removed 30 Traits
[INFO] [2021-04-19 10:08:51] ## remove_type: MetaTrait
[INFO] [2021-04-19 10:08:51] ++ Calling delete_all on 10 instances...
[INFO] [2021-04-19 10:08:51] [10:08:51.186] Removed 10 Metatraits
[INFO] [2021-04-19 10:08:51] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 10:08:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 10:08:51] [10:08:51.187] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 10:08:51] ## remove_type: Assoc
[INFO] [2021-04-19 10:08:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 10:08:51] [10:08:51.189] Removed 0 Assocs
[INFO] [2021-04-19 10:08:51] ## remove_type: MetaAssoc
[INFO] [2021-04-19 10:08:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 10:08:51] [10:08:51.190] Removed 0 Metaassocs
[INFO] [2021-04-19 10:08:51] ## remove_type: Identifier
[INFO] [2021-04-19 10:08:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 10:08:51] [10:08:51.191] Removed 0 Identifiers
[INFO] [2021-04-19 10:08:51] ## remove_type: Reference
[INFO] [2021-04-19 10:08:51] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 10:08:51] [10:08:51.193] Removed 0 References
[INFO] [2021-04-19 10:08:51] Starting batch with ID 86116152...
[INFO] [2021-04-19 10:08:51] Starting batch with ID 86116152...
[INFO] [2021-04-19 10:08:51] Starting batch with ID 86116152...
[INFO] [2021-04-19 10:08:51] ## remove_type: Node
[INFO] [2021-04-19 10:08:51] ++ Calling delete_all on 10 instances...
[INFO] [2021-04-19 10:08:51] [10:08:51.338] Removed 10 Nodes
[START] [2021-04-19 10:08:52] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 10:08:52] Creating resource from OpenData
[START] [2021-04-19 10:08:53] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 10:08:53] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 10:08:58] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 10:08:58] Creating resource from OpenData
[START] [2021-04-19 10:08:58] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 10:08:58] create_harvest_instance
[INFO] [2021-04-19 10:08:58] Created harvest instance #3724
[STOP] [2021-04-19 10:08:58] create_harvest_instance
[START] [2021-04-19 10:08:58] fetch_files
[STOP] [2021-04-19 10:08:58] fetch_files
[START] [2021-04-19 10:08:58] validate_each_file
[INFO] [2021-04-19 10:08:58] Looping over 4 formats...
[INFO] [2021-04-19 10:08:58] ...refs (/app/public/data/warrant_et_al_wa/references.tsv)
[INFO] [2021-04-19 10:08:58] Valid: /app/public/converted_csv/warrant_et_al_wa_refs_3724.csv (0 lines)
[INFO] [2021-04-19 10:08:58] ...nodes (/app/public/data/warrant_et_al_wa/taxa.txt)
[INFO] [2021-04-19 10:08:58] Valid: /app/public/converted_csv/warrant_et_al_wa_nodes_3724.csv (10 lines)
[INFO] [2021-04-19 10:08:58] ...occurrences (/app/public/data/warrant_et_al_wa/occurrences.txt)
[INFO] [2021-04-19 10:08:58] Valid: /app/public/converted_csv/warrant_et_al_wa_occurrences_3724.csv (10 lines)
[INFO] [2021-04-19 10:08:58] ...measurements (/app/public/data/warrant_et_al_wa/measurementsorfacts.txt)
[INFO] [2021-04-19 10:08:58] Valid: /app/public/converted_csv/warrant_et_al_wa_measurements_3724.csv (30 lines)
[STOP] [2021-04-19 10:08:58] validate_each_file
[START] [2021-04-19 10:08:58] convert_to_csv
[INFO] [2021-04-19 10:08:58] Looping over 4 formats...
[INFO] [2021-04-19 10:08:58] ...refs (/app/public/data/warrant_et_al_wa/references.tsv)
[CMD] [2021-04-19 10:08:58] /usr/bin/sort /app/public/converted_csv/warrant_et_al_wa_refs_3724.csv > /app/public/converted_csv/warrant_et_al_wa_refs_3724.csv_sorted
[INFO] [2021-04-19 10:08:58] Converted: /app/public/converted_csv/warrant_et_al_wa_refs_3724.csv (0 lines)
[INFO] [2021-04-19 10:08:58] ...nodes (/app/public/data/warrant_et_al_wa/taxa.txt)
[CMD] [2021-04-19 10:08:58] /usr/bin/sort /app/public/converted_csv/warrant_et_al_wa_nodes_3724.csv > /app/public/converted_csv/warrant_et_al_wa_nodes_3724.csv_sorted
[INFO] [2021-04-19 10:08:59] Converted: /app/public/converted_csv/warrant_et_al_wa_nodes_3724.csv (10 lines)
[INFO] [2021-04-19 10:08:59] ...occurrences (/app/public/data/warrant_et_al_wa/occurrences.txt)
[CMD] [2021-04-19 10:08:59] /usr/bin/sort /app/public/converted_csv/warrant_et_al_wa_occurrences_3724.csv > /app/public/converted_csv/warrant_et_al_wa_occurrences_3724.csv_sorted
[INFO] [2021-04-19 10:08:59] Converted: /app/public/converted_csv/warrant_et_al_wa_occurrences_3724.csv (10 lines)
[INFO] [2021-04-19 10:08:59] ...measurements (/app/public/data/warrant_et_al_wa/measurementsorfacts.txt)
[CMD] [2021-04-19 10:08:59] /usr/bin/sort /app/public/converted_csv/warrant_et_al_wa_measurements_3724.csv > /app/public/converted_csv/warrant_et_al_wa_measurements_3724.csv_sorted
[INFO] [2021-04-19 10:09:00] Converted: /app/public/converted_csv/warrant_et_al_wa_measurements_3724.csv (30 lines)
[STOP] [2021-04-19 10:09:00] convert_to_csv
[START] [2021-04-19 10:09:00] calculate_delta
[INFO] [2021-04-19 10:09:00] Looping over 4 formats...
[INFO] [2021-04-19 10:09:00] ...refs (/app/public/data/warrant_et_al_wa/references.tsv)
[CMD] [2021-04-19 10:09:00] echo "0a" > /app/public/diff/warrant_et_al_wa_refs_3724.diff
[CMD] [2021-04-19 10:09:00] tail -n +1 /app/public/converted_csv/warrant_et_al_wa_refs_3724.csv >> /app/public/diff/warrant_et_al_wa_refs_3724.diff
[CMD] [2021-04-19 10:09:00] echo "." >> /app/public/diff/warrant_et_al_wa_refs_3724.diff
[INFO] [2021-04-19 10:09:01] Created diff: /app/public/diff/warrant_et_al_wa_refs_3724.diff (2 lines)
[INFO] [2021-04-19 10:09:01] ...nodes (/app/public/data/warrant_et_al_wa/taxa.txt)
[CMD] [2021-04-19 10:09:01] echo "0a" > /app/public/diff/warrant_et_al_wa_nodes_3724.diff
[CMD] [2021-04-19 10:09:01] tail -n +1 /app/public/converted_csv/warrant_et_al_wa_nodes_3724.csv >> /app/public/diff/warrant_et_al_wa_nodes_3724.diff
[CMD] [2021-04-19 10:09:01] echo "." >> /app/public/diff/warrant_et_al_wa_nodes_3724.diff
[INFO] [2021-04-19 10:09:02] Created diff: /app/public/diff/warrant_et_al_wa_nodes_3724.diff (12 lines)
[INFO] [2021-04-19 10:09:02] ...occurrences (/app/public/data/warrant_et_al_wa/occurrences.txt)
[CMD] [2021-04-19 10:09:02] echo "0a" > /app/public/diff/warrant_et_al_wa_occurrences_3724.diff
[CMD] [2021-04-19 10:09:02] tail -n +1 /app/public/converted_csv/warrant_et_al_wa_occurrences_3724.csv >> /app/public/diff/warrant_et_al_wa_occurrences_3724.diff
[CMD] [2021-04-19 10:09:03] echo "." >> /app/public/diff/warrant_et_al_wa_occurrences_3724.diff
[INFO] [2021-04-19 10:09:03] Created diff: /app/public/diff/warrant_et_al_wa_occurrences_3724.diff (12 lines)
[INFO] [2021-04-19 10:09:03] ...measurements (/app/public/data/warrant_et_al_wa/measurementsorfacts.txt)
[CMD] [2021-04-19 10:09:03] echo "0a" > /app/public/diff/warrant_et_al_wa_measurements_3724.diff
[CMD] [2021-04-19 10:09:03] tail -n +1 /app/public/converted_csv/warrant_et_al_wa_measurements_3724.csv >> /app/public/diff/warrant_et_al_wa_measurements_3724.diff
[CMD] [2021-04-19 10:09:04] echo "." >> /app/public/diff/warrant_et_al_wa_measurements_3724.diff
[INFO] [2021-04-19 10:09:04] Created diff: /app/public/diff/warrant_et_al_wa_measurements_3724.diff (32 lines)
[STOP] [2021-04-19 10:09:04] calculate_delta
[START] [2021-04-19 10:09:04] parse_diff_and_store
[INFO] [2021-04-19 10:09:04] Handling diff: /app/public/diff/warrant_et_al_wa_refs_3724.diff (2 lines)
[INFO] [2021-04-19 10:09:04] Loading refs diff file into memory (2 /app/public/diff/warrant_et_al_wa_refs_3724.diff lines)...
[INFO] [2021-04-19 10:09:05] Handling diff: /app/public/diff/warrant_et_al_wa_nodes_3724.diff (12 lines)
[INFO] [2021-04-19 10:09:05] Loading nodes diff file into memory (12 /app/public/diff/warrant_et_al_wa_nodes_3724.diff lines)...
[INFO] [2021-04-19 10:09:06] Handling diff: /app/public/diff/warrant_et_al_wa_occurrences_3724.diff (12 lines)
[INFO] [2021-04-19 10:09:06] Loading occurrences diff file into memory (12 /app/public/diff/warrant_et_al_wa_occurrences_3724.diff lines)...
[INFO] [2021-04-19 10:09:06] Handling diff: /app/public/diff/warrant_et_al_wa_measurements_3724.diff (32 lines)
[INFO] [2021-04-19 10:09:07] Loading measurements diff file into memory (32 /app/public/diff/warrant_et_al_wa_measurements_3724.diff lines)...
[INFO] [2021-04-19 10:09:07] Storing 10 ScientificNames
[INFO] [2021-04-19 10:09:07] Processing group of 10 in 1 groups of 1000
[INFO] [2021-04-19 10:09:07] Average Time: 0.0
[INFO] [2021-04-19 10:09:07] Total Time: 1s
[INFO] [2021-04-19 10:09:07] Storing 10 Nodes
[INFO] [2021-04-19 10:09:07] Processing group of 10 in 1 groups of 1000
[INFO] [2021-04-19 10:09:07] Average Time: 0.0
[INFO] [2021-04-19 10:09:07] Total Time: 1s
[INFO] [2021-04-19 10:09:07] Storing 10 Occurrences
[INFO] [2021-04-19 10:09:07] Processing group of 10 in 1 groups of 1000
[INFO] [2021-04-19 10:09:07] Average Time: 0.0
[INFO] [2021-04-19 10:09:07] Total Time: 1s
[INFO] [2021-04-19 10:09:07] Storing 30 Traits
[INFO] [2021-04-19 10:09:07] Processing group of 30 in 1 groups of 1000
[INFO] [2021-04-19 10:09:07] Average Time: 0.01
[INFO] [2021-04-19 10:09:07] Total Time: 1s
[INFO] [2021-04-19 10:09:07] Storing 10 MetaTraits
[INFO] [2021-04-19 10:09:07] Processing group of 10 in 1 groups of 1000
[INFO] [2021-04-19 10:09:07] Average Time: 0.0
[INFO] [2021-04-19 10:09:07] Total Time: 1s
[STOP] [2021-04-19 10:09:07] parse_diff_and_store
[START] [2021-04-19 10:09:07] resolve_keys
[INFO] [2021-04-19 10:09:13] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 10:09:13] traits to occurrences...
[INFO] [2021-04-19 10:09:13] traits to nodes (through occurrences)...
[INFO] [2021-04-19 10:09:13] Traits to sex term...
[INFO] [2021-04-19 10:09:13] Traits to lifestage term...
[INFO] [2021-04-19 10:09:13] MetaTraits to traits...
[INFO] [2021-04-19 10:09:13] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 10:09:13] Assocs to occurrences...
[INFO] [2021-04-19 10:09:13] Assocs to nodes...
[INFO] [2021-04-19 10:09:13] Assoc to sex term...
[INFO] [2021-04-19 10:09:13] Assoc to lifestage term...
[INFO] [2021-04-19 10:09:13] MetaAssoc to assocs...
[STOP] [2021-04-19 10:09:13] resolve_keys
[START] [2021-04-19 10:09:13] hold_for_later_1
[STOP] [2021-04-19 10:09:13] hold_for_later_1
[START] [2021-04-19 10:09:13] hold_for_later_2
[STOP] [2021-04-19 10:09:13] hold_for_later_2
[START] [2021-04-19 10:09:13] resolve_missing_parents
[STOP] [2021-04-19 10:09:13] resolve_missing_parents
[START] [2021-04-19 10:09:13] rebuild_nodes
[START] [2021-04-19 10:09:13] Flattener#flatten
[START] [2021-04-19 10:09:13] Flattener#study_resource
[START] [2021-04-19 10:09:13] Flattener#build_ancestry
[STOP] [2021-04-19 10:09:13] Flattener#build_ancestry
[INFO] [2021-04-19 10:09:13] 10 ancestry keys
[START] [2021-04-19 10:09:13] build_node_ancestors
[INFO] [2021-04-19 10:09:13] old ancestors deleted.
[STOP] [2021-04-19 10:09:13] build_node_ancestors
[WARN] [2021-04-19 10:09:13] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 10:09:13] Flattener#flatten
[STOP] [2021-04-19 10:09:13] rebuild_nodes
[START] [2021-04-19 10:09:13] resolve_missing_media_owners
[STOP] [2021-04-19 10:09:13] resolve_missing_media_owners
[START] [2021-04-19 10:09:13] sanitize_media_verbatims
[STOP] [2021-04-19 10:09:13] sanitize_media_verbatims
[START] [2021-04-19 10:09:13] queue_downloads
[STOP] [2021-04-19 10:09:13] queue_downloads
[START] [2021-04-19 10:09:13] parse_names
[WARN] [2021-04-19 10:09:13] I see 10 names which still need to be parsed.
[STOP] [2021-04-19 10:09:15] parse_names
[START] [2021-04-19 10:09:15] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 10:09:15] denormalize_canonical_names_to_nodes
[START] [2021-04-19 10:09:15] match_nodes
[START] [2021-04-19 10:09:15] map_all_nodes_to_pages
[STOP] [2021-04-19 10:09:15] map_all_nodes_to_pages
[INFO] [2021-04-19 10:09:15] ZERO unmatched nodes (of 10)! Nicely done.
[START] [2021-04-19 10:09:15] update_nodes
[STOP] [2021-04-19 10:09:15] update_nodes
[STOP] [2021-04-19 10:09:15] match_nodes
[START] [2021-04-19 10:09:15] reindex_search
[STOP] [2021-04-19 10:09:15] reindex_search
[START] [2021-04-19 10:09:15] normalize_units
[STOP] [2021-04-19 10:09:15] normalize_units
[START] [2021-04-19 10:09:15] calculate_statistics
[2021-04-19 10:09:15] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 10:09:15] calculate_statistics
[START] [2021-04-19 10:09:15] complete_harvest_instance
[START] [2021-04-19 10:09:15] overall_tsv_creation
[INFO] [2021-04-19 10:09:15] Processing group of 10 in 1 batches of 10000
[INFO] [2021-04-19 10:09:51] 10 Traits (unfiltered)...
[INFO] [2021-04-19 10:10:25] 10 Traits (filtered)...
[INFO] [2021-04-19 10:10:25] 0 Associations (filtered)...
[INFO] [2021-04-19 10:10:25] 20 metadata added.
[INFO] [2021-04-19 10:10:25] 0 metadata added.
[INFO] [2021-04-19 10:10:52] Average Time: 72.7
[INFO] [2021-04-19 10:10:52] Total Time: 1m38s
[STOP] [2021-04-19 10:10:52] overall_tsv_creation
[INFO] [2021-04-19 10:10:52] Done. Check your files:
[INFO] [2021-04-19 10:10:52] (10 lines) /app/public/data/warrant_et_al_wa/publish_nodes.tsv
[INFO] [2021-04-19 10:10:52] (10 lines) /app/public/data/warrant_et_al_wa/publish_scientific_names.tsv
[INFO] [2021-04-19 10:10:53] (11 lines) /app/public/data/warrant_et_al_wa/publish_traits.tsv
[INFO] [2021-04-19 10:10:53] (21 lines) /app/public/data/warrant_et_al_wa/publish_metadata.tsv
[STOP] [2021-04-19 10:10:53] complete_harvest_instance
[START] [2021-04-19 10:10:53] completed
[STOP] [2021-04-19 10:10:53] completed
[STOP] [2021-04-19 10:10:53] logged process, took 115.73
[INFO] [2021-04-19 15:36:20] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:45:52] ## remove_type: ScientificName
[INFO] [2021-04-19 15:45:52] ++ Calling delete_all on 10 instances...
[INFO] [2021-04-19 15:45:52] [15:45:52.916] Removed 10 Scientificnames
[INFO] [2021-04-19 15:45:52] ## remove_type: Vernacular
[INFO] [2021-04-19 15:45:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:45:52] [15:45:52.917] Removed 0 Vernaculars
[INFO] [2021-04-19 15:45:52] ## remove_type: Article
[INFO] [2021-04-19 15:45:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:45:52] [15:45:52.919] Removed 0 Articles
[INFO] [2021-04-19 15:45:52] ## remove_type: Medium
[INFO] [2021-04-19 15:45:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:45:52] [15:45:52.921] Removed 0 Media
[INFO] [2021-04-19 15:45:52] ## remove_type: Trait
[INFO] [2021-04-19 15:45:52] ++ Calling delete_all on 30 instances...
[INFO] [2021-04-19 15:45:52] [15:45:52.924] Removed 30 Traits
[INFO] [2021-04-19 15:45:52] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:45:52] ++ Calling delete_all on 10 instances...
[INFO] [2021-04-19 15:45:52] [15:45:52.926] Removed 10 Metatraits
[INFO] [2021-04-19 15:45:52] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:45:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:45:52] [15:45:52.927] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:45:52] ## remove_type: Assoc
[INFO] [2021-04-19 15:45:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:45:52] [15:45:52.929] Removed 0 Assocs
[INFO] [2021-04-19 15:45:52] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:45:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:45:52] [15:45:52.930] Removed 0 Metaassocs
[INFO] [2021-04-19 15:45:52] ## remove_type: Identifier
[INFO] [2021-04-19 15:45:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:45:52] [15:45:52.931] Removed 0 Identifiers
[INFO] [2021-04-19 15:45:52] ## remove_type: Reference
[INFO] [2021-04-19 15:45:52] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:45:52] [15:45:52.933] Removed 0 References
[INFO] [2021-04-19 15:45:52] Starting batch with ID 92872665...
[INFO] [2021-04-19 15:45:52] Starting batch with ID 92872665...
[INFO] [2021-04-19 15:45:52] Starting batch with ID 92872665...
[INFO] [2021-04-19 15:45:52] Starting batch with ID 92872665...
[INFO] [2021-04-19 15:45:52] Starting batch with ID 92872665...
[INFO] [2021-04-19 15:45:52] ## remove_type: Node
[INFO] [2021-04-19 15:45:52] ++ Calling delete_all on 10 instances...
[INFO] [2021-04-19 15:45:52] [15:45:52.986] Removed 10 Nodes
[START] [2021-04-19 15:45:53] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:45:53] Creating resource from OpenData
[START] [2021-04-19 15:45:53] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:45:53] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:45:53] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:45:53] Creating resource from OpenData
[START] [2021-04-19 15:45:53] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:45:53] create_harvest_instance
[INFO] [2021-04-19 15:45:53] Created harvest instance #3777
[STOP] [2021-04-19 15:45:53] create_harvest_instance
[START] [2021-04-19 15:45:53] fetch_files
[STOP] [2021-04-19 15:45:53] fetch_files
[START] [2021-04-19 15:45:53] validate_each_file
[INFO] [2021-04-19 15:45:53] Looping over 4 formats...
[INFO] [2021-04-19 15:45:53] ...refs (/app/public/data/warrant_et_al_wa/references.tsv)
[INFO] [2021-04-19 15:45:53] Valid: /app/public/converted_csv/warrant_et_al_wa_refs_3777.csv (0 lines)
[INFO] [2021-04-19 15:45:53] ...nodes (/app/public/data/warrant_et_al_wa/taxa.txt)
[INFO] [2021-04-19 15:45:53] Valid: /app/public/converted_csv/warrant_et_al_wa_nodes_3777.csv (10 lines)
[INFO] [2021-04-19 15:45:53] ...occurrences (/app/public/data/warrant_et_al_wa/occurrences.txt)
[INFO] [2021-04-19 15:45:53] Valid: /app/public/converted_csv/warrant_et_al_wa_occurrences_3777.csv (10 lines)
[INFO] [2021-04-19 15:45:53] ...measurements (/app/public/data/warrant_et_al_wa/measurementsorfacts.txt)
[INFO] [2021-04-19 15:45:53] Valid: /app/public/converted_csv/warrant_et_al_wa_measurements_3777.csv (30 lines)
[STOP] [2021-04-19 15:45:53] validate_each_file
[START] [2021-04-19 15:45:53] convert_to_csv
[INFO] [2021-04-19 15:45:53] Looping over 4 formats...
[INFO] [2021-04-19 15:45:53] ...refs (/app/public/data/warrant_et_al_wa/references.tsv)
[CMD] [2021-04-19 15:45:53] /usr/bin/sort /app/public/converted_csv/warrant_et_al_wa_refs_3777.csv > /app/public/converted_csv/warrant_et_al_wa_refs_3777.csv_sorted
[INFO] [2021-04-19 15:45:53] Converted: /app/public/converted_csv/warrant_et_al_wa_refs_3777.csv (0 lines)
[INFO] [2021-04-19 15:45:53] ...nodes (/app/public/data/warrant_et_al_wa/taxa.txt)
[CMD] [2021-04-19 15:45:53] /usr/bin/sort /app/public/converted_csv/warrant_et_al_wa_nodes_3777.csv > /app/public/converted_csv/warrant_et_al_wa_nodes_3777.csv_sorted
[INFO] [2021-04-19 15:45:53] Converted: /app/public/converted_csv/warrant_et_al_wa_nodes_3777.csv (10 lines)
[INFO] [2021-04-19 15:45:53] ...occurrences (/app/public/data/warrant_et_al_wa/occurrences.txt)
[CMD] [2021-04-19 15:45:53] /usr/bin/sort /app/public/converted_csv/warrant_et_al_wa_occurrences_3777.csv > /app/public/converted_csv/warrant_et_al_wa_occurrences_3777.csv_sorted
[INFO] [2021-04-19 15:45:53] Converted: /app/public/converted_csv/warrant_et_al_wa_occurrences_3777.csv (10 lines)
[INFO] [2021-04-19 15:45:53] ...measurements (/app/public/data/warrant_et_al_wa/measurementsorfacts.txt)
[CMD] [2021-04-19 15:45:53] /usr/bin/sort /app/public/converted_csv/warrant_et_al_wa_measurements_3777.csv > /app/public/converted_csv/warrant_et_al_wa_measurements_3777.csv_sorted
[INFO] [2021-04-19 15:45:53] Converted: /app/public/converted_csv/warrant_et_al_wa_measurements_3777.csv (30 lines)
[STOP] [2021-04-19 15:45:53] convert_to_csv
[START] [2021-04-19 15:45:53] calculate_delta
[INFO] [2021-04-19 15:45:53] Looping over 4 formats...
[INFO] [2021-04-19 15:45:53] ...refs (/app/public/data/warrant_et_al_wa/references.tsv)
[CMD] [2021-04-19 15:45:53] echo "0a" > /app/public/diff/warrant_et_al_wa_refs_3777.diff
[CMD] [2021-04-19 15:45:53] tail -n +1 /app/public/converted_csv/warrant_et_al_wa_refs_3777.csv >> /app/public/diff/warrant_et_al_wa_refs_3777.diff
[CMD] [2021-04-19 15:45:53] echo "." >> /app/public/diff/warrant_et_al_wa_refs_3777.diff
[INFO] [2021-04-19 15:45:53] Created diff: /app/public/diff/warrant_et_al_wa_refs_3777.diff (2 lines)
[INFO] [2021-04-19 15:45:53] ...nodes (/app/public/data/warrant_et_al_wa/taxa.txt)
[CMD] [2021-04-19 15:45:53] echo "0a" > /app/public/diff/warrant_et_al_wa_nodes_3777.diff
[CMD] [2021-04-19 15:45:53] tail -n +1 /app/public/converted_csv/warrant_et_al_wa_nodes_3777.csv >> /app/public/diff/warrant_et_al_wa_nodes_3777.diff
[CMD] [2021-04-19 15:45:53] echo "." >> /app/public/diff/warrant_et_al_wa_nodes_3777.diff
[INFO] [2021-04-19 15:45:53] Created diff: /app/public/diff/warrant_et_al_wa_nodes_3777.diff (12 lines)
[INFO] [2021-04-19 15:45:53] ...occurrences (/app/public/data/warrant_et_al_wa/occurrences.txt)
[CMD] [2021-04-19 15:45:53] echo "0a" > /app/public/diff/warrant_et_al_wa_occurrences_3777.diff
[CMD] [2021-04-19 15:45:53] tail -n +1 /app/public/converted_csv/warrant_et_al_wa_occurrences_3777.csv >> /app/public/diff/warrant_et_al_wa_occurrences_3777.diff
[CMD] [2021-04-19 15:45:53] echo "." >> /app/public/diff/warrant_et_al_wa_occurrences_3777.diff
[INFO] [2021-04-19 15:45:53] Created diff: /app/public/diff/warrant_et_al_wa_occurrences_3777.diff (12 lines)
[INFO] [2021-04-19 15:45:53] ...measurements (/app/public/data/warrant_et_al_wa/measurementsorfacts.txt)
[CMD] [2021-04-19 15:45:53] echo "0a" > /app/public/diff/warrant_et_al_wa_measurements_3777.diff
[CMD] [2021-04-19 15:45:53] tail -n +1 /app/public/converted_csv/warrant_et_al_wa_measurements_3777.csv >> /app/public/diff/warrant_et_al_wa_measurements_3777.diff
[CMD] [2021-04-19 15:45:53] echo "." >> /app/public/diff/warrant_et_al_wa_measurements_3777.diff
[INFO] [2021-04-19 15:45:53] Created diff: /app/public/diff/warrant_et_al_wa_measurements_3777.diff (32 lines)
[STOP] [2021-04-19 15:45:53] calculate_delta
[START] [2021-04-19 15:45:53] parse_diff_and_store
[INFO] [2021-04-19 15:45:53] Handling diff: /app/public/diff/warrant_et_al_wa_refs_3777.diff (2 lines)
[INFO] [2021-04-19 15:45:53] Loading refs diff file into memory (2 /app/public/diff/warrant_et_al_wa_refs_3777.diff lines)...
[INFO] [2021-04-19 15:45:53] Handling diff: /app/public/diff/warrant_et_al_wa_nodes_3777.diff (12 lines)
[INFO] [2021-04-19 15:45:53] Loading nodes diff file into memory (12 /app/public/diff/warrant_et_al_wa_nodes_3777.diff lines)...
[INFO] [2021-04-19 15:45:53] Handling diff: /app/public/diff/warrant_et_al_wa_occurrences_3777.diff (12 lines)
[INFO] [2021-04-19 15:45:53] Loading occurrences diff file into memory (12 /app/public/diff/warrant_et_al_wa_occurrences_3777.diff lines)...
[INFO] [2021-04-19 15:45:53] Handling diff: /app/public/diff/warrant_et_al_wa_measurements_3777.diff (32 lines)
[INFO] [2021-04-19 15:45:53] Loading measurements diff file into memory (32 /app/public/diff/warrant_et_al_wa_measurements_3777.diff lines)...
[INFO] [2021-04-19 15:45:53] Storing 10 ScientificNames
[INFO] [2021-04-19 15:45:53] Processing group of 10 in 1 groups of 1000
[INFO] [2021-04-19 15:45:53] Average Time: 0.0
[INFO] [2021-04-19 15:45:53] Total Time: 1s
[INFO] [2021-04-19 15:45:53] Storing 10 Nodes
[INFO] [2021-04-19 15:45:53] Processing group of 10 in 1 groups of 1000
[INFO] [2021-04-19 15:45:53] Average Time: 0.0
[INFO] [2021-04-19 15:45:53] Total Time: 1s
[INFO] [2021-04-19 15:45:53] Storing 10 Occurrences
[INFO] [2021-04-19 15:45:53] Processing group of 10 in 1 groups of 1000
[INFO] [2021-04-19 15:45:53] Average Time: 0.0
[INFO] [2021-04-19 15:45:53] Total Time: 1s
[INFO] [2021-04-19 15:45:53] Storing 30 Traits
[INFO] [2021-04-19 15:45:53] Processing group of 30 in 1 groups of 1000
[INFO] [2021-04-19 15:45:53] Average Time: 0.01
[INFO] [2021-04-19 15:45:53] Total Time: 1s
[INFO] [2021-04-19 15:45:53] Storing 10 MetaTraits
[INFO] [2021-04-19 15:45:53] Processing group of 10 in 1 groups of 1000
[INFO] [2021-04-19 15:45:53] Average Time: 0.0
[INFO] [2021-04-19 15:45:53] Total Time: 1s
[STOP] [2021-04-19 15:45:53] parse_diff_and_store
[START] [2021-04-19 15:45:53] resolve_keys
[INFO] [2021-04-19 15:45:59] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:45:59] traits to occurrences...
[INFO] [2021-04-19 15:45:59] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:45:59] Traits to sex term...
[INFO] [2021-04-19 15:45:59] Traits to lifestage term...
[INFO] [2021-04-19 15:45:59] MetaTraits to traits...
[INFO] [2021-04-19 15:45:59] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:45:59] Assocs to occurrences...
[INFO] [2021-04-19 15:45:59] Assocs to nodes...
[INFO] [2021-04-19 15:45:59] Assoc to sex term...
[INFO] [2021-04-19 15:45:59] Assoc to lifestage term...
[INFO] [2021-04-19 15:45:59] MetaAssoc to assocs...
[STOP] [2021-04-19 15:45:59] resolve_keys
[START] [2021-04-19 15:45:59] hold_for_later_1
[STOP] [2021-04-19 15:45:59] hold_for_later_1
[START] [2021-04-19 15:45:59] hold_for_later_2
[STOP] [2021-04-19 15:45:59] hold_for_later_2
[START] [2021-04-19 15:45:59] resolve_missing_parents
[STOP] [2021-04-19 15:45:59] resolve_missing_parents
[START] [2021-04-19 15:45:59] rebuild_nodes
[START] [2021-04-19 15:45:59] Flattener#flatten
[START] [2021-04-19 15:45:59] Flattener#study_resource
[START] [2021-04-19 15:45:59] Flattener#build_ancestry
[STOP] [2021-04-19 15:45:59] Flattener#build_ancestry
[INFO] [2021-04-19 15:45:59] 10 ancestry keys
[START] [2021-04-19 15:45:59] build_node_ancestors
[INFO] [2021-04-19 15:45:59] old ancestors deleted.
[STOP] [2021-04-19 15:45:59] build_node_ancestors
[WARN] [2021-04-19 15:45:59] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:45:59] Flattener#flatten
[STOP] [2021-04-19 15:45:59] rebuild_nodes
[START] [2021-04-19 15:45:59] resolve_missing_media_owners
[STOP] [2021-04-19 15:45:59] resolve_missing_media_owners
[START] [2021-04-19 15:45:59] sanitize_media_verbatims
[STOP] [2021-04-19 15:45:59] sanitize_media_verbatims
[START] [2021-04-19 15:45:59] queue_downloads
[STOP] [2021-04-19 15:45:59] queue_downloads
[START] [2021-04-19 15:45:59] parse_names
[WARN] [2021-04-19 15:45:59] I see 10 names which still need to be parsed.
[STOP] [2021-04-19 15:46:00] parse_names
[START] [2021-04-19 15:46:00] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:46:00] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:46:00] match_nodes
[START] [2021-04-19 15:46:00] map_all_nodes_to_pages
[STOP] [2021-04-19 15:46:00] map_all_nodes_to_pages
[INFO] [2021-04-19 15:46:00] ZERO unmatched nodes (of 10)! Nicely done.
[START] [2021-04-19 15:46:00] update_nodes
[STOP] [2021-04-19 15:46:00] update_nodes
[STOP] [2021-04-19 15:46:00] match_nodes
[START] [2021-04-19 15:46:00] reindex_search
[STOP] [2021-04-19 15:46:01] reindex_search
[START] [2021-04-19 15:46:01] normalize_units
[STOP] [2021-04-19 15:46:01] normalize_units
[START] [2021-04-19 15:46:01] calculate_statistics
[2021-04-19 15:46:01] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:46:01] calculate_statistics
[START] [2021-04-19 15:46:01] complete_harvest_instance
[START] [2021-04-19 15:46:01] overall_tsv_creation
[INFO] [2021-04-19 15:46:01] Processing group of 10 in 1 batches of 10000
[INFO] [2021-04-19 15:46:37] 10 Traits (unfiltered)...
[INFO] [2021-04-19 15:47:11] 10 Traits (filtered)...
[INFO] [2021-04-19 15:47:11] 0 Associations (filtered)...
[INFO] [2021-04-19 15:47:11] 20 metadata added.
[INFO] [2021-04-19 15:47:11] 0 metadata added.
[INFO] [2021-04-19 15:47:37] Average Time: 72.18
[INFO] [2021-04-19 15:47:37] Total Time: 1m37s
[STOP] [2021-04-19 15:47:37] overall_tsv_creation
[INFO] [2021-04-19 15:47:37] Done. Check your files:
[INFO] [2021-04-19 15:47:37] (10 lines) /app/public/data/warrant_et_al_wa/publish_nodes.tsv
[INFO] [2021-04-19 15:47:37] (10 lines) /app/public/data/warrant_et_al_wa/publish_scientific_names.tsv
[INFO] [2021-04-19 15:47:37] (11 lines) /app/public/data/warrant_et_al_wa/publish_traits.tsv
[INFO] [2021-04-19 15:47:37] (21 lines) /app/public/data/warrant_et_al_wa/publish_metadata.tsv
[STOP] [2021-04-19 15:47:37] complete_harvest_instance
[START] [2021-04-19 15:47:37] completed
[STOP] [2021-04-19 15:47:37] completed
[STOP] [2021-04-19 15:47:37] logged process, took 104.19

Latest Process