Stage:
completed
Fetched:
19 Apr 15:14
Validated:
19 Apr 15:14
Deltas Created
19 Apr 15:14
Units Normalized:
19 Apr 15:14
Ancestry Built:
19 Apr 15:14
Nodes Matched:
19 Apr 15:14
Names Parsed:
19 Apr 15:14
New Models Stored:
19 Apr 15:14
Indexed:
19 Apr 15:14
Completed:
19 Apr 15:16
Time to Harvest:
less than a minute
Harvesting Log
(422 lines)
# Logfile created on 2020-08-27 15:26:15 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:26:15] logged process
[START] [2020-08-27 15:26:15] Creating resource from OpenData
[START] [2020-08-27 15:26:15] logged process
[START] [2020-08-27 15:26:15] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:26:15] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:26:15] Creating resource from OpenData
[INFO] [2020-11-19 13:52:13] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 13:52:18] ## remove_type: ScientificName
[INFO] [2020-11-19 13:52:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:52:18] [13:52:18.243] Removed 0 Scientificnames
[INFO] [2020-11-19 13:52:18] ## remove_type: Vernacular
[INFO] [2020-11-19 13:52:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:52:18] [13:52:18.246] Removed 0 Vernaculars
[INFO] [2020-11-19 13:52:18] ## remove_type: Article
[INFO] [2020-11-19 13:52:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:52:18] [13:52:18.249] Removed 0 Articles
[INFO] [2020-11-19 13:52:18] ## remove_type: Medium
[INFO] [2020-11-19 13:52:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:52:18] [13:52:18.253] Removed 0 Media
[INFO] [2020-11-19 13:52:18] ## remove_type: Trait
[INFO] [2020-11-19 13:52:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:52:18] [13:52:18.256] Removed 0 Traits
[INFO] [2020-11-19 13:52:18] ## remove_type: MetaTrait
[INFO] [2020-11-19 13:52:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:52:18] [13:52:18.258] Removed 0 Metatraits
[INFO] [2020-11-19 13:52:18] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 13:52:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:52:18] [13:52:18.261] Removed 0 Occurrencemetadata
[INFO] [2020-11-19 13:52:18] ## remove_type: Assoc
[INFO] [2020-11-19 13:52:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:52:18] [13:52:18.264] Removed 0 Assocs
[INFO] [2020-11-19 13:52:18] ## remove_type: MetaAssoc
[INFO] [2020-11-19 13:52:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:52:18] [13:52:18.266] Removed 0 Metaassocs
[INFO] [2020-11-19 13:52:18] ## remove_type: Identifier
[INFO] [2020-11-19 13:52:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:52:18] [13:52:18.269] Removed 0 Identifiers
[INFO] [2020-11-19 13:52:18] ## remove_type: Reference
[INFO] [2020-11-19 13:52:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:52:18] [13:52:18.271] Removed 0 References
[INFO] [2020-11-19 13:52:18] ## remove_type: Node
[INFO] [2020-11-19 13:52:18] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:52:18] [13:52:18.293] Removed 0 Nodes
[START] [2020-11-19 13:52:18] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 13:52:18] Creating resource from OpenData
[START] [2020-11-19 13:52:18] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 13:52:18] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:52:18] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:52:18] Creating resource from OpenData
[START] [2020-11-19 13:52:18] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 13:52:18] create_harvest_instance
[STOP] [2020-11-19 13:52:20] create_harvest_instance
[START] [2020-11-19 13:52:20] fetch_files
[STOP] [2020-11-19 13:52:20] fetch_files
[START] [2020-11-19 13:52:20] validate_each_file
[STOP] [2020-11-19 13:52:20] validate_each_file
[START] [2020-11-19 13:52:20] convert_to_csv
[CMD] [2020-11-19 13:52:20] /usr/bin/sort /app/public/converted_csv/beckers_et_al_be_refs_24470.csv > /app/public/converted_csv/beckers_et_al_be_refs_24470.csv_sorted
[CMD] [2020-11-19 13:52:20] /usr/bin/sort /app/public/converted_csv/beckers_et_al_be_nodes_24471.csv > /app/public/converted_csv/beckers_et_al_be_nodes_24471.csv_sorted
[CMD] [2020-11-19 13:52:20] /usr/bin/sort /app/public/converted_csv/beckers_et_al_be_occurrences_24472.csv > /app/public/converted_csv/beckers_et_al_be_occurrences_24472.csv_sorted
[CMD] [2020-11-19 13:52:20] /usr/bin/sort /app/public/converted_csv/beckers_et_al_be_measurements_24473.csv > /app/public/converted_csv/beckers_et_al_be_measurements_24473.csv_sorted
[STOP] [2020-11-19 13:52:20] convert_to_csv
[START] [2020-11-19 13:52:20] calculate_delta
[CMD] [2020-11-19 13:52:20] echo "0a" > /app/public/diff/beckers_et_al_be_refs_24470.diff
[CMD] [2020-11-19 13:52:20] tail -n +1 /app/public/converted_csv/beckers_et_al_be_refs_24470.csv >> /app/public/diff/beckers_et_al_be_refs_24470.diff
[CMD] [2020-11-19 13:52:20] echo "." >> /app/public/diff/beckers_et_al_be_refs_24470.diff
[CMD] [2020-11-19 13:52:20] echo "0a" > /app/public/diff/beckers_et_al_be_nodes_24471.diff
[CMD] [2020-11-19 13:52:20] tail -n +1 /app/public/converted_csv/beckers_et_al_be_nodes_24471.csv >> /app/public/diff/beckers_et_al_be_nodes_24471.diff
[CMD] [2020-11-19 13:52:20] echo "." >> /app/public/diff/beckers_et_al_be_nodes_24471.diff
[CMD] [2020-11-19 13:52:20] echo "0a" > /app/public/diff/beckers_et_al_be_occurrences_24472.diff
[CMD] [2020-11-19 13:52:20] tail -n +1 /app/public/converted_csv/beckers_et_al_be_occurrences_24472.csv >> /app/public/diff/beckers_et_al_be_occurrences_24472.diff
[CMD] [2020-11-19 13:52:20] echo "." >> /app/public/diff/beckers_et_al_be_occurrences_24472.diff
[CMD] [2020-11-19 13:52:20] echo "0a" > /app/public/diff/beckers_et_al_be_measurements_24473.diff
[CMD] [2020-11-19 13:52:20] tail -n +1 /app/public/converted_csv/beckers_et_al_be_measurements_24473.csv >> /app/public/diff/beckers_et_al_be_measurements_24473.diff
[CMD] [2020-11-19 13:52:20] echo "." >> /app/public/diff/beckers_et_al_be_measurements_24473.diff
[STOP] [2020-11-19 13:52:20] calculate_delta
[START] [2020-11-19 13:52:20] parse_diff_and_store
[INFO] [2020-11-19 13:52:20] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 13:52:20] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 13:52:20] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 13:52:21] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-19 13:52:21] Storing 1 ScientificNames
[INFO] [2020-11-19 13:52:21] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:52:21] Average Time: 0.0
[INFO] [2020-11-19 13:52:21] Total Time: 1s
[INFO] [2020-11-19 13:52:21] Storing 1 Nodes
[INFO] [2020-11-19 13:52:21] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:52:21] Average Time: 0.0
[INFO] [2020-11-19 13:52:21] Total Time: 1s
[INFO] [2020-11-19 13:52:21] Storing 2 Occurrences
[INFO] [2020-11-19 13:52:21] Processing group of 2 in 1 groups of 1000
[INFO] [2020-11-19 13:52:21] Average Time: 0.0
[INFO] [2020-11-19 13:52:21] Total Time: 1s
[INFO] [2020-11-19 13:52:21] Storing 2 OccurrenceMetadata
[INFO] [2020-11-19 13:52:21] Processing group of 2 in 1 groups of 1000
[INFO] [2020-11-19 13:52:21] Average Time: 0.0
[INFO] [2020-11-19 13:52:21] Total Time: 1s
[INFO] [2020-11-19 13:52:21] Storing 4 Traits
[INFO] [2020-11-19 13:52:21] Processing group of 4 in 1 groups of 1000
[INFO] [2020-11-19 13:52:21] Average Time: 0.01
[INFO] [2020-11-19 13:52:21] Total Time: 1s
[INFO] [2020-11-19 13:52:21] Storing 2 MetaTraits
[INFO] [2020-11-19 13:52:21] Processing group of 2 in 1 groups of 1000
[INFO] [2020-11-19 13:52:21] Average Time: 0.0
[INFO] [2020-11-19 13:52:21] Total Time: 1s
[STOP] [2020-11-19 13:52:21] parse_diff_and_store
[START] [2020-11-19 13:52:21] resolve_keys
[INFO] [2020-11-19 13:52:27] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-19 13:52:27] traits to occurrences...
[INFO] [2020-11-19 13:52:27] traits to nodes (through occurrences)...
[INFO] [2020-11-19 13:52:27] Traits to sex term...
[INFO] [2020-11-19 13:52:27] Traits to lifestage term...
[INFO] [2020-11-19 13:52:27] MetaTraits to traits...
[INFO] [2020-11-19 13:52:27] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-19 13:52:27] Assocs to occurrences...
[INFO] [2020-11-19 13:52:27] Assocs to nodes...
[INFO] [2020-11-19 13:52:27] Assoc to sex term...
[INFO] [2020-11-19 13:52:27] Assoc to lifestage term...
[INFO] [2020-11-19 13:52:27] MetaAssoc to assocs...
[STOP] [2020-11-19 13:52:27] resolve_keys
[START] [2020-11-19 13:52:27] hold_for_later_1
[STOP] [2020-11-19 13:52:27] hold_for_later_1
[START] [2020-11-19 13:52:27] hold_for_later_2
[STOP] [2020-11-19 13:52:27] hold_for_later_2
[START] [2020-11-19 13:52:27] resolve_missing_parents
[STOP] [2020-11-19 13:52:27] resolve_missing_parents
[START] [2020-11-19 13:52:27] rebuild_nodes
[START] [2020-11-19 13:52:27] Flattener#flatten
[START] [2020-11-19 13:52:27] Flattener#study_resource
[START] [2020-11-19 13:52:27] Flattener#build_ancestry
[STOP] [2020-11-19 13:52:27] Flattener#build_ancestry
[INFO] [2020-11-19 13:52:27] 1 ancestry keys
[START] [2020-11-19 13:52:27] build_node_ancestors
[INFO] [2020-11-19 13:52:27] old ancestors deleted.
[STOP] [2020-11-19 13:52:27] build_node_ancestors
[WARN] [2020-11-19 13:52:27] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-19 13:52:27] Flattener#flatten
[STOP] [2020-11-19 13:52:27] rebuild_nodes
[START] [2020-11-19 13:52:27] resolve_missing_media_owners
[STOP] [2020-11-19 13:52:27] resolve_missing_media_owners
[START] [2020-11-19 13:52:27] sanitize_media_verbatims
[STOP] [2020-11-19 13:52:27] sanitize_media_verbatims
[START] [2020-11-19 13:52:27] queue_downloads
[STOP] [2020-11-19 13:52:27] queue_downloads
[START] [2020-11-19 13:52:27] parse_names
[WARN] [2020-11-19 13:52:27] I see 1 names which still need to be parsed.
[STOP] [2020-11-19 13:52:28] parse_names
[START] [2020-11-19 13:52:28] denormalize_canonical_names_to_nodes
[STOP] [2020-11-19 13:52:28] denormalize_canonical_names_to_nodes
[START] [2020-11-19 13:52:28] match_nodes
[START] [2020-11-19 13:52:28] map_all_nodes_to_pages
[STOP] [2020-11-19 13:52:28] map_all_nodes_to_pages
[INFO] [2020-11-19 13:52:28] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-11-19 13:52:28] update_nodes
[STOP] [2020-11-19 13:52:28] update_nodes
[STOP] [2020-11-19 13:52:28] match_nodes
[START] [2020-11-19 13:52:28] reindex_search
[STOP] [2020-11-19 13:52:28] reindex_search
[START] [2020-11-19 13:52:28] normalize_units
[STOP] [2020-11-19 13:52:28] normalize_units
[START] [2020-11-19 13:52:28] calculate_statistics
[2020-11-19 13:52:28] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-19 13:52:28] calculate_statistics
[START] [2020-11-19 13:52:28] complete_harvest_instance
[START] [2020-11-19 13:52:28] overall_tsv_creation
[INFO] [2020-11-19 13:52:28] Processing group of 1 in 1 batches of 10000
[INFO] [2020-11-19 13:53:11] 2 Traits (unfiltered)...
[INFO] [2020-11-19 13:53:54] 2 Traits (filtered)...
[INFO] [2020-11-19 13:53:54] 0 Associations (filtered)...
[INFO] [2020-11-19 13:53:54] 6 metadata added.
[INFO] [2020-11-19 13:53:54] 0 metadata added.
[INFO] [2020-11-19 13:53:54] Average Time: 65.52
[INFO] [2020-11-19 13:53:54] Total Time: 1m26s
[STOP] [2020-11-19 13:53:54] overall_tsv_creation
[INFO] [2020-11-19 13:53:54] Done. Check your files:
[INFO] [2020-11-19 13:53:54] (1 lines) /app/public/data/beckers_et_al_be/publish_nodes.tsv
[INFO] [2020-11-19 13:53:54] (1 lines) /app/public/data/beckers_et_al_be/publish_scientific_names.tsv
[INFO] [2020-11-19 13:53:54] (3 lines) /app/public/data/beckers_et_al_be/publish_traits.tsv
[INFO] [2020-11-19 13:53:54] (5 lines) /app/public/data/beckers_et_al_be/publish_metadata.tsv
[STOP] [2020-11-19 13:53:54] complete_harvest_instance
[START] [2020-11-19 13:53:54] completed
[STOP] [2020-11-19 13:53:54] completed
[STOP] [2020-11-19 13:53:54] logged process, took 95.47
[INFO] [2021-04-19 15:14:33] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:14:37] ## remove_type: ScientificName
[INFO] [2021-04-19 15:14:37] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:14:37] [15:14:37.921] Removed 1 Scientificnames
[INFO] [2021-04-19 15:14:37] ## remove_type: Vernacular
[INFO] [2021-04-19 15:14:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:14:37] [15:14:37.922] Removed 0 Vernaculars
[INFO] [2021-04-19 15:14:37] ## remove_type: Article
[INFO] [2021-04-19 15:14:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:14:37] [15:14:37.923] Removed 0 Articles
[INFO] [2021-04-19 15:14:37] ## remove_type: Medium
[INFO] [2021-04-19 15:14:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:14:37] [15:14:37.925] Removed 0 Media
[INFO] [2021-04-19 15:14:37] ## remove_type: Trait
[INFO] [2021-04-19 15:14:37] ++ Calling delete_all on 4 instances...
[INFO] [2021-04-19 15:14:37] [15:14:37.927] Removed 4 Traits
[INFO] [2021-04-19 15:14:37] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:14:37] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:14:37] [15:14:37.929] Removed 2 Metatraits
[INFO] [2021-04-19 15:14:37] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:14:37] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:14:37] [15:14:37.930] Removed 2 Occurrencemetadata
[INFO] [2021-04-19 15:14:37] ## remove_type: Assoc
[INFO] [2021-04-19 15:14:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:14:37] [15:14:37.932] Removed 0 Assocs
[INFO] [2021-04-19 15:14:37] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:14:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:14:37] [15:14:37.933] Removed 0 Metaassocs
[INFO] [2021-04-19 15:14:37] ## remove_type: Identifier
[INFO] [2021-04-19 15:14:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:14:37] [15:14:37.935] Removed 0 Identifiers
[INFO] [2021-04-19 15:14:37] ## remove_type: Reference
[INFO] [2021-04-19 15:14:37] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:14:37] [15:14:37.936] Removed 0 References
[INFO] [2021-04-19 15:14:37] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:37] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:37] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:37] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:37] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:37] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:37] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:37] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] Starting batch with ID 84620787...
[INFO] [2021-04-19 15:14:38] ## remove_type: Node
[INFO] [2021-04-19 15:14:38] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:14:38] [15:14:38.117] Removed 1 Nodes
[START] [2021-04-19 15:14:38] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:14:38] Creating resource from OpenData
[START] [2021-04-19 15:14:38] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:14:38] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:14:38] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:14:38] Creating resource from OpenData
[START] [2021-04-19 15:14:38] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:14:38] create_harvest_instance
[INFO] [2021-04-19 15:14:38] Created harvest instance #3759
[STOP] [2021-04-19 15:14:38] create_harvest_instance
[START] [2021-04-19 15:14:38] fetch_files
[STOP] [2021-04-19 15:14:38] fetch_files
[START] [2021-04-19 15:14:38] validate_each_file
[INFO] [2021-04-19 15:14:38] Looping over 4 formats...
[INFO] [2021-04-19 15:14:38] ...refs (/app/public/data/beckers_et_al_be/references.tsv)
[INFO] [2021-04-19 15:14:38] Valid: /app/public/converted_csv/beckers_et_al_be_refs_3759.csv (0 lines)
[INFO] [2021-04-19 15:14:38] ...nodes (/app/public/data/beckers_et_al_be/taxa.txt)
[INFO] [2021-04-19 15:14:38] Valid: /app/public/converted_csv/beckers_et_al_be_nodes_3759.csv (1 lines)
[INFO] [2021-04-19 15:14:38] ...occurrences (/app/public/data/beckers_et_al_be/occurrences.txt)
[INFO] [2021-04-19 15:14:38] Valid: /app/public/converted_csv/beckers_et_al_be_occurrences_3759.csv (2 lines)
[INFO] [2021-04-19 15:14:38] ...measurements (/app/public/data/beckers_et_al_be/measurementsorfacts.txt)
[INFO] [2021-04-19 15:14:38] Valid: /app/public/converted_csv/beckers_et_al_be_measurements_3759.csv (4 lines)
[STOP] [2021-04-19 15:14:38] validate_each_file
[START] [2021-04-19 15:14:38] convert_to_csv
[INFO] [2021-04-19 15:14:38] Looping over 4 formats...
[INFO] [2021-04-19 15:14:38] ...refs (/app/public/data/beckers_et_al_be/references.tsv)
[CMD] [2021-04-19 15:14:38] /usr/bin/sort /app/public/converted_csv/beckers_et_al_be_refs_3759.csv > /app/public/converted_csv/beckers_et_al_be_refs_3759.csv_sorted
[INFO] [2021-04-19 15:14:38] Converted: /app/public/converted_csv/beckers_et_al_be_refs_3759.csv (0 lines)
[INFO] [2021-04-19 15:14:38] ...nodes (/app/public/data/beckers_et_al_be/taxa.txt)
[CMD] [2021-04-19 15:14:38] /usr/bin/sort /app/public/converted_csv/beckers_et_al_be_nodes_3759.csv > /app/public/converted_csv/beckers_et_al_be_nodes_3759.csv_sorted
[INFO] [2021-04-19 15:14:38] Converted: /app/public/converted_csv/beckers_et_al_be_nodes_3759.csv (1 lines)
[INFO] [2021-04-19 15:14:38] ...occurrences (/app/public/data/beckers_et_al_be/occurrences.txt)
[CMD] [2021-04-19 15:14:38] /usr/bin/sort /app/public/converted_csv/beckers_et_al_be_occurrences_3759.csv > /app/public/converted_csv/beckers_et_al_be_occurrences_3759.csv_sorted
[INFO] [2021-04-19 15:14:38] Converted: /app/public/converted_csv/beckers_et_al_be_occurrences_3759.csv (2 lines)
[INFO] [2021-04-19 15:14:38] ...measurements (/app/public/data/beckers_et_al_be/measurementsorfacts.txt)
[CMD] [2021-04-19 15:14:38] /usr/bin/sort /app/public/converted_csv/beckers_et_al_be_measurements_3759.csv > /app/public/converted_csv/beckers_et_al_be_measurements_3759.csv_sorted
[INFO] [2021-04-19 15:14:38] Converted: /app/public/converted_csv/beckers_et_al_be_measurements_3759.csv (4 lines)
[STOP] [2021-04-19 15:14:38] convert_to_csv
[START] [2021-04-19 15:14:38] calculate_delta
[INFO] [2021-04-19 15:14:38] Looping over 4 formats...
[INFO] [2021-04-19 15:14:38] ...refs (/app/public/data/beckers_et_al_be/references.tsv)
[CMD] [2021-04-19 15:14:38] echo "0a" > /app/public/diff/beckers_et_al_be_refs_3759.diff
[CMD] [2021-04-19 15:14:38] tail -n +1 /app/public/converted_csv/beckers_et_al_be_refs_3759.csv >> /app/public/diff/beckers_et_al_be_refs_3759.diff
[CMD] [2021-04-19 15:14:38] echo "." >> /app/public/diff/beckers_et_al_be_refs_3759.diff
[INFO] [2021-04-19 15:14:38] Created diff: /app/public/diff/beckers_et_al_be_refs_3759.diff (2 lines)
[INFO] [2021-04-19 15:14:38] ...nodes (/app/public/data/beckers_et_al_be/taxa.txt)
[CMD] [2021-04-19 15:14:38] echo "0a" > /app/public/diff/beckers_et_al_be_nodes_3759.diff
[CMD] [2021-04-19 15:14:38] tail -n +1 /app/public/converted_csv/beckers_et_al_be_nodes_3759.csv >> /app/public/diff/beckers_et_al_be_nodes_3759.diff
[CMD] [2021-04-19 15:14:38] echo "." >> /app/public/diff/beckers_et_al_be_nodes_3759.diff
[INFO] [2021-04-19 15:14:38] Created diff: /app/public/diff/beckers_et_al_be_nodes_3759.diff (3 lines)
[INFO] [2021-04-19 15:14:38] ...occurrences (/app/public/data/beckers_et_al_be/occurrences.txt)
[CMD] [2021-04-19 15:14:38] echo "0a" > /app/public/diff/beckers_et_al_be_occurrences_3759.diff
[CMD] [2021-04-19 15:14:38] tail -n +1 /app/public/converted_csv/beckers_et_al_be_occurrences_3759.csv >> /app/public/diff/beckers_et_al_be_occurrences_3759.diff
[CMD] [2021-04-19 15:14:38] echo "." >> /app/public/diff/beckers_et_al_be_occurrences_3759.diff
[INFO] [2021-04-19 15:14:38] Created diff: /app/public/diff/beckers_et_al_be_occurrences_3759.diff (4 lines)
[INFO] [2021-04-19 15:14:38] ...measurements (/app/public/data/beckers_et_al_be/measurementsorfacts.txt)
[CMD] [2021-04-19 15:14:38] echo "0a" > /app/public/diff/beckers_et_al_be_measurements_3759.diff
[CMD] [2021-04-19 15:14:38] tail -n +1 /app/public/converted_csv/beckers_et_al_be_measurements_3759.csv >> /app/public/diff/beckers_et_al_be_measurements_3759.diff
[CMD] [2021-04-19 15:14:38] echo "." >> /app/public/diff/beckers_et_al_be_measurements_3759.diff
[INFO] [2021-04-19 15:14:38] Created diff: /app/public/diff/beckers_et_al_be_measurements_3759.diff (6 lines)
[STOP] [2021-04-19 15:14:38] calculate_delta
[START] [2021-04-19 15:14:38] parse_diff_and_store
[INFO] [2021-04-19 15:14:38] Handling diff: /app/public/diff/beckers_et_al_be_refs_3759.diff (2 lines)
[INFO] [2021-04-19 15:14:38] Loading refs diff file into memory (2 /app/public/diff/beckers_et_al_be_refs_3759.diff lines)...
[INFO] [2021-04-19 15:14:38] Handling diff: /app/public/diff/beckers_et_al_be_nodes_3759.diff (3 lines)
[INFO] [2021-04-19 15:14:38] Loading nodes diff file into memory (3 /app/public/diff/beckers_et_al_be_nodes_3759.diff lines)...
[INFO] [2021-04-19 15:14:38] Handling diff: /app/public/diff/beckers_et_al_be_occurrences_3759.diff (4 lines)
[INFO] [2021-04-19 15:14:38] Loading occurrences diff file into memory (4 /app/public/diff/beckers_et_al_be_occurrences_3759.diff lines)...
[INFO] [2021-04-19 15:14:38] Handling diff: /app/public/diff/beckers_et_al_be_measurements_3759.diff (6 lines)
[INFO] [2021-04-19 15:14:38] Loading measurements diff file into memory (6 /app/public/diff/beckers_et_al_be_measurements_3759.diff lines)...
[INFO] [2021-04-19 15:14:38] Storing 1 ScientificNames
[INFO] [2021-04-19 15:14:38] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:14:38] Average Time: 0.0
[INFO] [2021-04-19 15:14:38] Total Time: 1s
[INFO] [2021-04-19 15:14:38] Storing 1 Nodes
[INFO] [2021-04-19 15:14:38] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:14:38] Average Time: 0.0
[INFO] [2021-04-19 15:14:38] Total Time: 1s
[INFO] [2021-04-19 15:14:38] Storing 2 Occurrences
[INFO] [2021-04-19 15:14:38] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:14:38] Average Time: 0.0
[INFO] [2021-04-19 15:14:38] Total Time: 1s
[INFO] [2021-04-19 15:14:38] Storing 2 OccurrenceMetadata
[INFO] [2021-04-19 15:14:38] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:14:38] Average Time: 0.0
[INFO] [2021-04-19 15:14:38] Total Time: 1s
[INFO] [2021-04-19 15:14:38] Storing 4 Traits
[INFO] [2021-04-19 15:14:38] Processing group of 4 in 1 groups of 1000
[INFO] [2021-04-19 15:14:38] Average Time: 0.0
[INFO] [2021-04-19 15:14:38] Total Time: 1s
[INFO] [2021-04-19 15:14:38] Storing 2 MetaTraits
[INFO] [2021-04-19 15:14:38] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:14:38] Average Time: 0.0
[INFO] [2021-04-19 15:14:38] Total Time: 1s
[STOP] [2021-04-19 15:14:38] parse_diff_and_store
[START] [2021-04-19 15:14:38] resolve_keys
[INFO] [2021-04-19 15:14:44] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:14:44] traits to occurrences...
[INFO] [2021-04-19 15:14:44] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:14:44] Traits to sex term...
[INFO] [2021-04-19 15:14:44] Traits to lifestage term...
[INFO] [2021-04-19 15:14:44] MetaTraits to traits...
[INFO] [2021-04-19 15:14:44] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:14:44] Assocs to occurrences...
[INFO] [2021-04-19 15:14:44] Assocs to nodes...
[INFO] [2021-04-19 15:14:44] Assoc to sex term...
[INFO] [2021-04-19 15:14:44] Assoc to lifestage term...
[INFO] [2021-04-19 15:14:44] MetaAssoc to assocs...
[STOP] [2021-04-19 15:14:44] resolve_keys
[START] [2021-04-19 15:14:44] hold_for_later_1
[STOP] [2021-04-19 15:14:44] hold_for_later_1
[START] [2021-04-19 15:14:44] hold_for_later_2
[STOP] [2021-04-19 15:14:44] hold_for_later_2
[START] [2021-04-19 15:14:44] resolve_missing_parents
[STOP] [2021-04-19 15:14:44] resolve_missing_parents
[START] [2021-04-19 15:14:44] rebuild_nodes
[START] [2021-04-19 15:14:44] Flattener#flatten
[START] [2021-04-19 15:14:44] Flattener#study_resource
[START] [2021-04-19 15:14:44] Flattener#build_ancestry
[STOP] [2021-04-19 15:14:44] Flattener#build_ancestry
[INFO] [2021-04-19 15:14:44] 1 ancestry keys
[START] [2021-04-19 15:14:44] build_node_ancestors
[INFO] [2021-04-19 15:14:44] old ancestors deleted.
[STOP] [2021-04-19 15:14:44] build_node_ancestors
[WARN] [2021-04-19 15:14:44] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:14:44] Flattener#flatten
[STOP] [2021-04-19 15:14:44] rebuild_nodes
[START] [2021-04-19 15:14:44] resolve_missing_media_owners
[STOP] [2021-04-19 15:14:44] resolve_missing_media_owners
[START] [2021-04-19 15:14:44] sanitize_media_verbatims
[STOP] [2021-04-19 15:14:44] sanitize_media_verbatims
[START] [2021-04-19 15:14:44] queue_downloads
[STOP] [2021-04-19 15:14:44] queue_downloads
[START] [2021-04-19 15:14:44] parse_names
[WARN] [2021-04-19 15:14:44] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 15:14:45] parse_names
[START] [2021-04-19 15:14:45] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:14:45] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:14:45] match_nodes
[START] [2021-04-19 15:14:45] map_all_nodes_to_pages
[STOP] [2021-04-19 15:14:45] map_all_nodes_to_pages
[INFO] [2021-04-19 15:14:46] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 15:14:46] update_nodes
[STOP] [2021-04-19 15:14:46] update_nodes
[STOP] [2021-04-19 15:14:46] match_nodes
[START] [2021-04-19 15:14:46] reindex_search
[STOP] [2021-04-19 15:14:46] reindex_search
[START] [2021-04-19 15:14:46] normalize_units
[STOP] [2021-04-19 15:14:46] normalize_units
[START] [2021-04-19 15:14:46] calculate_statistics
[2021-04-19 15:14:46] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:14:46] calculate_statistics
[START] [2021-04-19 15:14:46] complete_harvest_instance
[START] [2021-04-19 15:14:46] overall_tsv_creation
[INFO] [2021-04-19 15:14:46] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 15:15:21] 2 Traits (unfiltered)...
[INFO] [2021-04-19 15:15:52] 2 Traits (filtered)...
[INFO] [2021-04-19 15:15:52] 0 Associations (filtered)...
[INFO] [2021-04-19 15:15:52] 2 metadata added.
[INFO] [2021-04-19 15:15:52] 0 metadata added.
[INFO] [2021-04-19 15:16:17] Average Time: 67.65
[INFO] [2021-04-19 15:16:17] Total Time: 1m32s
[STOP] [2021-04-19 15:16:17] overall_tsv_creation
[INFO] [2021-04-19 15:16:17] Done. Check your files:
[INFO] [2021-04-19 15:16:17] (1 lines) /app/public/data/beckers_et_al_be/publish_nodes.tsv
[INFO] [2021-04-19 15:16:17] (1 lines) /app/public/data/beckers_et_al_be/publish_scientific_names.tsv
[INFO] [2021-04-19 15:16:17] (3 lines) /app/public/data/beckers_et_al_be/publish_traits.tsv
[INFO] [2021-04-19 15:16:17] (3 lines) /app/public/data/beckers_et_al_be/publish_metadata.tsv
[STOP] [2021-04-19 15:16:17] complete_harvest_instance
[START] [2021-04-19 15:16:17] completed
[STOP] [2021-04-19 15:16:17] completed
[STOP] [2021-04-19 15:16:17] logged process, took 99.1
Latest Process