Stage:
completed
Fetched:
19 Apr 15:40
Validated:
19 Apr 15:40
Deltas Created
19 Apr 15:40
Units Normalized:
19 Apr 15:40
Ancestry Built:
19 Apr 15:40
Nodes Matched:
19 Apr 15:40
Names Parsed:
19 Apr 15:40
New Models Stored:
19 Apr 15:40
Indexed:
19 Apr 15:40
Completed:
19 Apr 15:42
Time to Harvest:
less than a minute
Harvesting Log
(399 lines)
# Logfile created on 2020-08-27 15:44:10 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:44:10] logged process
[START] [2020-08-27 15:44:10] Creating resource from OpenData
[START] [2020-08-27 15:44:10] logged process
[START] [2020-08-27 15:44:10] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:44:10] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:44:10] Creating resource from OpenData
[INFO] [2020-12-03 11:36:01] ## HARVEST: type = -harvest
[START] [2020-12-03 11:36:03] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-03 11:36:03] create_harvest_instance
[STOP] [2020-12-03 11:36:04] create_harvest_instance
[START] [2020-12-03 11:36:04] fetch_files
[STOP] [2020-12-03 11:36:04] fetch_files
[START] [2020-12-03 11:36:04] validate_each_file
[STOP] [2020-12-03 11:36:04] validate_each_file
[START] [2020-12-03 11:36:04] convert_to_csv
[CMD] [2020-12-03 11:36:04] /usr/bin/sort /app/public/converted_csv/tshudy_et_al_tsh_refs_24828.csv > /app/public/converted_csv/tshudy_et_al_tsh_refs_24828.csv_sorted
[CMD] [2020-12-03 11:36:04] /usr/bin/sort /app/public/converted_csv/tshudy_et_al_tsh_nodes_24829.csv > /app/public/converted_csv/tshudy_et_al_tsh_nodes_24829.csv_sorted
[CMD] [2020-12-03 11:36:04] /usr/bin/sort /app/public/converted_csv/tshudy_et_al_tsh_occurrences_24830.csv > /app/public/converted_csv/tshudy_et_al_tsh_occurrences_24830.csv_sorted
[CMD] [2020-12-03 11:36:04] /usr/bin/sort /app/public/converted_csv/tshudy_et_al_tsh_measurements_24831.csv > /app/public/converted_csv/tshudy_et_al_tsh_measurements_24831.csv_sorted
[STOP] [2020-12-03 11:36:04] convert_to_csv
[START] [2020-12-03 11:36:04] calculate_delta
[CMD] [2020-12-03 11:36:04] echo "0a" > /app/public/diff/tshudy_et_al_tsh_refs_24828.diff
[CMD] [2020-12-03 11:36:04] tail -n +1 /app/public/converted_csv/tshudy_et_al_tsh_refs_24828.csv >> /app/public/diff/tshudy_et_al_tsh_refs_24828.diff
[CMD] [2020-12-03 11:36:04] echo "." >> /app/public/diff/tshudy_et_al_tsh_refs_24828.diff
[CMD] [2020-12-03 11:36:04] echo "0a" > /app/public/diff/tshudy_et_al_tsh_nodes_24829.diff
[CMD] [2020-12-03 11:36:04] tail -n +1 /app/public/converted_csv/tshudy_et_al_tsh_nodes_24829.csv >> /app/public/diff/tshudy_et_al_tsh_nodes_24829.diff
[CMD] [2020-12-03 11:36:04] echo "." >> /app/public/diff/tshudy_et_al_tsh_nodes_24829.diff
[CMD] [2020-12-03 11:36:04] echo "0a" > /app/public/diff/tshudy_et_al_tsh_occurrences_24830.diff
[CMD] [2020-12-03 11:36:04] tail -n +1 /app/public/converted_csv/tshudy_et_al_tsh_occurrences_24830.csv >> /app/public/diff/tshudy_et_al_tsh_occurrences_24830.diff
[CMD] [2020-12-03 11:36:04] echo "." >> /app/public/diff/tshudy_et_al_tsh_occurrences_24830.diff
[CMD] [2020-12-03 11:36:04] echo "0a" > /app/public/diff/tshudy_et_al_tsh_measurements_24831.diff
[CMD] [2020-12-03 11:36:04] tail -n +1 /app/public/converted_csv/tshudy_et_al_tsh_measurements_24831.csv >> /app/public/diff/tshudy_et_al_tsh_measurements_24831.diff
[CMD] [2020-12-03 11:36:04] echo "." >> /app/public/diff/tshudy_et_al_tsh_measurements_24831.diff
[STOP] [2020-12-03 11:36:04] calculate_delta
[START] [2020-12-03 11:36:04] parse_diff_and_store
[INFO] [2020-12-03 11:36:04] Loading refs diff file into memory (true lines)...
[INFO] [2020-12-03 11:36:05] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-03 11:36:05] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-03 11:36:05] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-03 11:36:05] Storing 1 ScientificNames
[INFO] [2020-12-03 11:36:05] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:36:05] Average Time: 0.0
[INFO] [2020-12-03 11:36:05] Total Time: 1s
[INFO] [2020-12-03 11:36:05] Storing 1 Nodes
[INFO] [2020-12-03 11:36:05] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:36:05] Average Time: 0.0
[INFO] [2020-12-03 11:36:05] Total Time: 1s
[INFO] [2020-12-03 11:36:05] Storing 1 Occurrences
[INFO] [2020-12-03 11:36:05] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:36:05] Average Time: 0.0
[INFO] [2020-12-03 11:36:05] Total Time: 1s
[INFO] [2020-12-03 11:36:05] Storing 2 Traits
[INFO] [2020-12-03 11:36:05] Processing group of 2 in 1 groups of 1000
[INFO] [2020-12-03 11:36:06] Average Time: 0.0
[INFO] [2020-12-03 11:36:06] Total Time: 1s
[INFO] [2020-12-03 11:36:06] Storing 1 MetaTraits
[INFO] [2020-12-03 11:36:06] Processing group of 1 in 1 groups of 1000
[INFO] [2020-12-03 11:36:06] Average Time: 0.0
[INFO] [2020-12-03 11:36:06] Total Time: 1s
[STOP] [2020-12-03 11:36:06] parse_diff_and_store
[START] [2020-12-03 11:36:06] resolve_keys
[INFO] [2020-12-03 11:36:11] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-03 11:36:11] traits to occurrences...
[INFO] [2020-12-03 11:36:11] traits to nodes (through occurrences)...
[INFO] [2020-12-03 11:36:11] Traits to sex term...
[INFO] [2020-12-03 11:36:11] Traits to lifestage term...
[INFO] [2020-12-03 11:36:11] MetaTraits to traits...
[INFO] [2020-12-03 11:36:11] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-03 11:36:11] Assocs to occurrences...
[INFO] [2020-12-03 11:36:11] Assocs to nodes...
[INFO] [2020-12-03 11:36:11] Assoc to sex term...
[INFO] [2020-12-03 11:36:11] Assoc to lifestage term...
[INFO] [2020-12-03 11:36:11] MetaAssoc to assocs...
[STOP] [2020-12-03 11:36:11] resolve_keys
[START] [2020-12-03 11:36:11] hold_for_later_1
[STOP] [2020-12-03 11:36:11] hold_for_later_1
[START] [2020-12-03 11:36:11] hold_for_later_2
[STOP] [2020-12-03 11:36:11] hold_for_later_2
[START] [2020-12-03 11:36:11] resolve_missing_parents
[STOP] [2020-12-03 11:36:11] resolve_missing_parents
[START] [2020-12-03 11:36:11] rebuild_nodes
[START] [2020-12-03 11:36:11] Flattener#flatten
[START] [2020-12-03 11:36:11] Flattener#study_resource
[START] [2020-12-03 11:36:11] Flattener#build_ancestry
[STOP] [2020-12-03 11:36:11] Flattener#build_ancestry
[INFO] [2020-12-03 11:36:11] 1 ancestry keys
[START] [2020-12-03 11:36:11] build_node_ancestors
[INFO] [2020-12-03 11:36:11] old ancestors deleted.
[STOP] [2020-12-03 11:36:11] build_node_ancestors
[WARN] [2020-12-03 11:36:11] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-03 11:36:11] Flattener#flatten
[STOP] [2020-12-03 11:36:11] rebuild_nodes
[START] [2020-12-03 11:36:11] resolve_missing_media_owners
[STOP] [2020-12-03 11:36:11] resolve_missing_media_owners
[START] [2020-12-03 11:36:11] sanitize_media_verbatims
[STOP] [2020-12-03 11:36:11] sanitize_media_verbatims
[START] [2020-12-03 11:36:11] queue_downloads
[STOP] [2020-12-03 11:36:11] queue_downloads
[START] [2020-12-03 11:36:11] parse_names
[WARN] [2020-12-03 11:36:11] I see 1 names which still need to be parsed.
[STOP] [2020-12-03 11:36:12] parse_names
[START] [2020-12-03 11:36:12] denormalize_canonical_names_to_nodes
[STOP] [2020-12-03 11:36:12] denormalize_canonical_names_to_nodes
[START] [2020-12-03 11:36:12] match_nodes
[START] [2020-12-03 11:36:12] map_all_nodes_to_pages
[STOP] [2020-12-03 11:36:12] map_all_nodes_to_pages
[INFO] [2020-12-03 11:36:12] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-12-03 11:36:12] update_nodes
[STOP] [2020-12-03 11:36:12] update_nodes
[STOP] [2020-12-03 11:36:12] match_nodes
[START] [2020-12-03 11:36:12] reindex_search
[STOP] [2020-12-03 11:36:12] reindex_search
[START] [2020-12-03 11:36:12] normalize_units
[STOP] [2020-12-03 11:36:12] normalize_units
[START] [2020-12-03 11:36:12] calculate_statistics
[2020-12-03 11:36:12] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-03 11:36:12] calculate_statistics
[START] [2020-12-03 11:36:12] complete_harvest_instance
[START] [2020-12-03 11:36:12] overall_tsv_creation
[INFO] [2020-12-03 11:36:12] Processing group of 1 in 1 batches of 10000
[INFO] [2020-12-03 11:36:51] 1 Traits (unfiltered)...
[INFO] [2020-12-03 11:37:27] 1 Traits (filtered)...
[INFO] [2020-12-03 11:37:27] 0 Associations (filtered)...
[INFO] [2020-12-03 11:37:27] 2 metadata added.
[INFO] [2020-12-03 11:37:27] 0 metadata added.
[INFO] [2020-12-03 11:37:27] Average Time: 51.59
[INFO] [2020-12-03 11:37:27] Total Time: 1m15s
[STOP] [2020-12-03 11:37:27] overall_tsv_creation
[INFO] [2020-12-03 11:37:27] Done. Check your files:
[INFO] [2020-12-03 11:37:27] (1 lines) /app/public/data/tshudy_et_al_tsh/publish_nodes.tsv
[INFO] [2020-12-03 11:37:27] (1 lines) /app/public/data/tshudy_et_al_tsh/publish_scientific_names.tsv
[INFO] [2020-12-03 11:37:27] (2 lines) /app/public/data/tshudy_et_al_tsh/publish_traits.tsv
[INFO] [2020-12-03 11:37:27] (3 lines) /app/public/data/tshudy_et_al_tsh/publish_metadata.tsv
[STOP] [2020-12-03 11:37:27] complete_harvest_instance
[START] [2020-12-03 11:37:27] completed
[STOP] [2020-12-03 11:37:27] completed
[STOP] [2020-12-03 11:37:27] logged process, took 83.87
[INFO] [2021-04-19 15:36:07] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 15:40:34] ## remove_type: ScientificName
[INFO] [2021-04-19 15:40:34] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:40:34] [15:40:34.137] Removed 1 Scientificnames
[INFO] [2021-04-19 15:40:34] ## remove_type: Vernacular
[INFO] [2021-04-19 15:40:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:40:34] [15:40:34.139] Removed 0 Vernaculars
[INFO] [2021-04-19 15:40:34] ## remove_type: Article
[INFO] [2021-04-19 15:40:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:40:34] [15:40:34.140] Removed 0 Articles
[INFO] [2021-04-19 15:40:34] ## remove_type: Medium
[INFO] [2021-04-19 15:40:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:40:34] [15:40:34.141] Removed 0 Media
[INFO] [2021-04-19 15:40:34] ## remove_type: Trait
[INFO] [2021-04-19 15:40:34] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 15:40:34] [15:40:34.143] Removed 2 Traits
[INFO] [2021-04-19 15:40:34] ## remove_type: MetaTrait
[INFO] [2021-04-19 15:40:34] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:40:34] [15:40:34.145] Removed 1 Metatraits
[INFO] [2021-04-19 15:40:34] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 15:40:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:40:34] [15:40:34.147] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 15:40:34] ## remove_type: Assoc
[INFO] [2021-04-19 15:40:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:40:34] [15:40:34.148] Removed 0 Assocs
[INFO] [2021-04-19 15:40:34] ## remove_type: MetaAssoc
[INFO] [2021-04-19 15:40:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:40:34] [15:40:34.150] Removed 0 Metaassocs
[INFO] [2021-04-19 15:40:34] ## remove_type: Identifier
[INFO] [2021-04-19 15:40:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:40:34] [15:40:34.151] Removed 0 Identifiers
[INFO] [2021-04-19 15:40:34] ## remove_type: Reference
[INFO] [2021-04-19 15:40:34] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 15:40:34] [15:40:34.152] Removed 0 References
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] Starting batch with ID 86115923...
[INFO] [2021-04-19 15:40:34] ## remove_type: Node
[INFO] [2021-04-19 15:40:34] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 15:40:34] [15:40:34.525] Removed 1 Nodes
[START] [2021-04-19 15:40:34] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:40:34] Creating resource from OpenData
[START] [2021-04-19 15:40:34] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:40:34] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:40:34] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 15:40:34] Creating resource from OpenData
[START] [2021-04-19 15:40:34] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 15:40:34] create_harvest_instance
[INFO] [2021-04-19 15:40:34] Created harvest instance #3774
[STOP] [2021-04-19 15:40:34] create_harvest_instance
[START] [2021-04-19 15:40:34] fetch_files
[STOP] [2021-04-19 15:40:34] fetch_files
[START] [2021-04-19 15:40:34] validate_each_file
[INFO] [2021-04-19 15:40:34] Looping over 4 formats...
[INFO] [2021-04-19 15:40:34] ...refs (/app/public/data/tshudy_et_al_tsh/references.tsv)
[INFO] [2021-04-19 15:40:34] Valid: /app/public/converted_csv/tshudy_et_al_tsh_refs_3774.csv (0 lines)
[INFO] [2021-04-19 15:40:34] ...nodes (/app/public/data/tshudy_et_al_tsh/taxa.txt)
[INFO] [2021-04-19 15:40:34] Valid: /app/public/converted_csv/tshudy_et_al_tsh_nodes_3774.csv (1 lines)
[INFO] [2021-04-19 15:40:34] ...occurrences (/app/public/data/tshudy_et_al_tsh/occurrences.txt)
[INFO] [2021-04-19 15:40:34] Valid: /app/public/converted_csv/tshudy_et_al_tsh_occurrences_3774.csv (1 lines)
[INFO] [2021-04-19 15:40:34] ...measurements (/app/public/data/tshudy_et_al_tsh/measurementsorfacts.txt)
[INFO] [2021-04-19 15:40:34] Valid: /app/public/converted_csv/tshudy_et_al_tsh_measurements_3774.csv (2 lines)
[STOP] [2021-04-19 15:40:34] validate_each_file
[START] [2021-04-19 15:40:34] convert_to_csv
[INFO] [2021-04-19 15:40:34] Looping over 4 formats...
[INFO] [2021-04-19 15:40:34] ...refs (/app/public/data/tshudy_et_al_tsh/references.tsv)
[CMD] [2021-04-19 15:40:34] /usr/bin/sort /app/public/converted_csv/tshudy_et_al_tsh_refs_3774.csv > /app/public/converted_csv/tshudy_et_al_tsh_refs_3774.csv_sorted
[INFO] [2021-04-19 15:40:35] Converted: /app/public/converted_csv/tshudy_et_al_tsh_refs_3774.csv (0 lines)
[INFO] [2021-04-19 15:40:35] ...nodes (/app/public/data/tshudy_et_al_tsh/taxa.txt)
[CMD] [2021-04-19 15:40:35] /usr/bin/sort /app/public/converted_csv/tshudy_et_al_tsh_nodes_3774.csv > /app/public/converted_csv/tshudy_et_al_tsh_nodes_3774.csv_sorted
[INFO] [2021-04-19 15:40:35] Converted: /app/public/converted_csv/tshudy_et_al_tsh_nodes_3774.csv (1 lines)
[INFO] [2021-04-19 15:40:35] ...occurrences (/app/public/data/tshudy_et_al_tsh/occurrences.txt)
[CMD] [2021-04-19 15:40:35] /usr/bin/sort /app/public/converted_csv/tshudy_et_al_tsh_occurrences_3774.csv > /app/public/converted_csv/tshudy_et_al_tsh_occurrences_3774.csv_sorted
[INFO] [2021-04-19 15:40:35] Converted: /app/public/converted_csv/tshudy_et_al_tsh_occurrences_3774.csv (1 lines)
[INFO] [2021-04-19 15:40:35] ...measurements (/app/public/data/tshudy_et_al_tsh/measurementsorfacts.txt)
[CMD] [2021-04-19 15:40:35] /usr/bin/sort /app/public/converted_csv/tshudy_et_al_tsh_measurements_3774.csv > /app/public/converted_csv/tshudy_et_al_tsh_measurements_3774.csv_sorted
[INFO] [2021-04-19 15:40:35] Converted: /app/public/converted_csv/tshudy_et_al_tsh_measurements_3774.csv (2 lines)
[STOP] [2021-04-19 15:40:35] convert_to_csv
[START] [2021-04-19 15:40:35] calculate_delta
[INFO] [2021-04-19 15:40:35] Looping over 4 formats...
[INFO] [2021-04-19 15:40:35] ...refs (/app/public/data/tshudy_et_al_tsh/references.tsv)
[CMD] [2021-04-19 15:40:35] echo "0a" > /app/public/diff/tshudy_et_al_tsh_refs_3774.diff
[CMD] [2021-04-19 15:40:35] tail -n +1 /app/public/converted_csv/tshudy_et_al_tsh_refs_3774.csv >> /app/public/diff/tshudy_et_al_tsh_refs_3774.diff
[CMD] [2021-04-19 15:40:35] echo "." >> /app/public/diff/tshudy_et_al_tsh_refs_3774.diff
[INFO] [2021-04-19 15:40:35] Created diff: /app/public/diff/tshudy_et_al_tsh_refs_3774.diff (2 lines)
[INFO] [2021-04-19 15:40:35] ...nodes (/app/public/data/tshudy_et_al_tsh/taxa.txt)
[CMD] [2021-04-19 15:40:35] echo "0a" > /app/public/diff/tshudy_et_al_tsh_nodes_3774.diff
[CMD] [2021-04-19 15:40:35] tail -n +1 /app/public/converted_csv/tshudy_et_al_tsh_nodes_3774.csv >> /app/public/diff/tshudy_et_al_tsh_nodes_3774.diff
[CMD] [2021-04-19 15:40:35] echo "." >> /app/public/diff/tshudy_et_al_tsh_nodes_3774.diff
[INFO] [2021-04-19 15:40:35] Created diff: /app/public/diff/tshudy_et_al_tsh_nodes_3774.diff (3 lines)
[INFO] [2021-04-19 15:40:35] ...occurrences (/app/public/data/tshudy_et_al_tsh/occurrences.txt)
[CMD] [2021-04-19 15:40:35] echo "0a" > /app/public/diff/tshudy_et_al_tsh_occurrences_3774.diff
[CMD] [2021-04-19 15:40:35] tail -n +1 /app/public/converted_csv/tshudy_et_al_tsh_occurrences_3774.csv >> /app/public/diff/tshudy_et_al_tsh_occurrences_3774.diff
[CMD] [2021-04-19 15:40:35] echo "." >> /app/public/diff/tshudy_et_al_tsh_occurrences_3774.diff
[INFO] [2021-04-19 15:40:35] Created diff: /app/public/diff/tshudy_et_al_tsh_occurrences_3774.diff (3 lines)
[INFO] [2021-04-19 15:40:35] ...measurements (/app/public/data/tshudy_et_al_tsh/measurementsorfacts.txt)
[CMD] [2021-04-19 15:40:35] echo "0a" > /app/public/diff/tshudy_et_al_tsh_measurements_3774.diff
[CMD] [2021-04-19 15:40:35] tail -n +1 /app/public/converted_csv/tshudy_et_al_tsh_measurements_3774.csv >> /app/public/diff/tshudy_et_al_tsh_measurements_3774.diff
[CMD] [2021-04-19 15:40:35] echo "." >> /app/public/diff/tshudy_et_al_tsh_measurements_3774.diff
[INFO] [2021-04-19 15:40:35] Created diff: /app/public/diff/tshudy_et_al_tsh_measurements_3774.diff (4 lines)
[STOP] [2021-04-19 15:40:35] calculate_delta
[START] [2021-04-19 15:40:35] parse_diff_and_store
[INFO] [2021-04-19 15:40:35] Handling diff: /app/public/diff/tshudy_et_al_tsh_refs_3774.diff (2 lines)
[INFO] [2021-04-19 15:40:35] Loading refs diff file into memory (2 /app/public/diff/tshudy_et_al_tsh_refs_3774.diff lines)...
[INFO] [2021-04-19 15:40:35] Handling diff: /app/public/diff/tshudy_et_al_tsh_nodes_3774.diff (3 lines)
[INFO] [2021-04-19 15:40:35] Loading nodes diff file into memory (3 /app/public/diff/tshudy_et_al_tsh_nodes_3774.diff lines)...
[INFO] [2021-04-19 15:40:35] Handling diff: /app/public/diff/tshudy_et_al_tsh_occurrences_3774.diff (3 lines)
[INFO] [2021-04-19 15:40:35] Loading occurrences diff file into memory (3 /app/public/diff/tshudy_et_al_tsh_occurrences_3774.diff lines)...
[INFO] [2021-04-19 15:40:35] Handling diff: /app/public/diff/tshudy_et_al_tsh_measurements_3774.diff (4 lines)
[INFO] [2021-04-19 15:40:35] Loading measurements diff file into memory (4 /app/public/diff/tshudy_et_al_tsh_measurements_3774.diff lines)...
[INFO] [2021-04-19 15:40:35] Storing 1 ScientificNames
[INFO] [2021-04-19 15:40:35] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:40:35] Average Time: 0.0
[INFO] [2021-04-19 15:40:35] Total Time: 1s
[INFO] [2021-04-19 15:40:35] Storing 1 Nodes
[INFO] [2021-04-19 15:40:35] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:40:35] Average Time: 0.0
[INFO] [2021-04-19 15:40:35] Total Time: 1s
[INFO] [2021-04-19 15:40:35] Storing 1 Occurrences
[INFO] [2021-04-19 15:40:35] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:40:35] Average Time: 0.0
[INFO] [2021-04-19 15:40:35] Total Time: 1s
[INFO] [2021-04-19 15:40:35] Storing 2 Traits
[INFO] [2021-04-19 15:40:35] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 15:40:35] Average Time: 0.0
[INFO] [2021-04-19 15:40:35] Total Time: 1s
[INFO] [2021-04-19 15:40:35] Storing 1 MetaTraits
[INFO] [2021-04-19 15:40:35] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 15:40:35] Average Time: 0.0
[INFO] [2021-04-19 15:40:35] Total Time: 1s
[STOP] [2021-04-19 15:40:35] parse_diff_and_store
[START] [2021-04-19 15:40:35] resolve_keys
[INFO] [2021-04-19 15:40:41] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 15:40:41] traits to occurrences...
[INFO] [2021-04-19 15:40:41] traits to nodes (through occurrences)...
[INFO] [2021-04-19 15:40:41] Traits to sex term...
[INFO] [2021-04-19 15:40:41] Traits to lifestage term...
[INFO] [2021-04-19 15:40:41] MetaTraits to traits...
[INFO] [2021-04-19 15:40:41] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 15:40:41] Assocs to occurrences...
[INFO] [2021-04-19 15:40:41] Assocs to nodes...
[INFO] [2021-04-19 15:40:41] Assoc to sex term...
[INFO] [2021-04-19 15:40:41] Assoc to lifestage term...
[INFO] [2021-04-19 15:40:41] MetaAssoc to assocs...
[STOP] [2021-04-19 15:40:41] resolve_keys
[START] [2021-04-19 15:40:41] hold_for_later_1
[STOP] [2021-04-19 15:40:41] hold_for_later_1
[START] [2021-04-19 15:40:41] hold_for_later_2
[STOP] [2021-04-19 15:40:41] hold_for_later_2
[START] [2021-04-19 15:40:41] resolve_missing_parents
[STOP] [2021-04-19 15:40:41] resolve_missing_parents
[START] [2021-04-19 15:40:41] rebuild_nodes
[START] [2021-04-19 15:40:41] Flattener#flatten
[START] [2021-04-19 15:40:41] Flattener#study_resource
[START] [2021-04-19 15:40:41] Flattener#build_ancestry
[STOP] [2021-04-19 15:40:41] Flattener#build_ancestry
[INFO] [2021-04-19 15:40:41] 1 ancestry keys
[START] [2021-04-19 15:40:41] build_node_ancestors
[INFO] [2021-04-19 15:40:41] old ancestors deleted.
[STOP] [2021-04-19 15:40:41] build_node_ancestors
[WARN] [2021-04-19 15:40:41] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 15:40:41] Flattener#flatten
[STOP] [2021-04-19 15:40:41] rebuild_nodes
[START] [2021-04-19 15:40:41] resolve_missing_media_owners
[STOP] [2021-04-19 15:40:41] resolve_missing_media_owners
[START] [2021-04-19 15:40:41] sanitize_media_verbatims
[STOP] [2021-04-19 15:40:41] sanitize_media_verbatims
[START] [2021-04-19 15:40:41] queue_downloads
[STOP] [2021-04-19 15:40:41] queue_downloads
[START] [2021-04-19 15:40:41] parse_names
[WARN] [2021-04-19 15:40:41] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 15:40:42] parse_names
[START] [2021-04-19 15:40:42] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 15:40:42] denormalize_canonical_names_to_nodes
[START] [2021-04-19 15:40:42] match_nodes
[START] [2021-04-19 15:40:42] map_all_nodes_to_pages
[STOP] [2021-04-19 15:40:42] map_all_nodes_to_pages
[INFO] [2021-04-19 15:40:42] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 15:40:42] update_nodes
[STOP] [2021-04-19 15:40:42] update_nodes
[STOP] [2021-04-19 15:40:42] match_nodes
[START] [2021-04-19 15:40:42] reindex_search
[STOP] [2021-04-19 15:40:42] reindex_search
[START] [2021-04-19 15:40:42] normalize_units
[STOP] [2021-04-19 15:40:42] normalize_units
[START] [2021-04-19 15:40:42] calculate_statistics
[2021-04-19 15:40:42] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 15:40:42] calculate_statistics
[START] [2021-04-19 15:40:42] complete_harvest_instance
[START] [2021-04-19 15:40:42] overall_tsv_creation
[INFO] [2021-04-19 15:40:42] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 15:41:17] 1 Traits (unfiltered)...
[INFO] [2021-04-19 15:41:50] 1 Traits (filtered)...
[INFO] [2021-04-19 15:41:50] 0 Associations (filtered)...
[INFO] [2021-04-19 15:41:50] 1 metadata added.
[INFO] [2021-04-19 15:41:50] 0 metadata added.
[INFO] [2021-04-19 15:42:17] Average Time: 71.54
[INFO] [2021-04-19 15:42:17] Total Time: 1m36s
[STOP] [2021-04-19 15:42:17] overall_tsv_creation
[INFO] [2021-04-19 15:42:17] Done. Check your files:
[INFO] [2021-04-19 15:42:17] (1 lines) /app/public/data/tshudy_et_al_tsh/publish_nodes.tsv
[INFO] [2021-04-19 15:42:17] (1 lines) /app/public/data/tshudy_et_al_tsh/publish_scientific_names.tsv
[INFO] [2021-04-19 15:42:17] (2 lines) /app/public/data/tshudy_et_al_tsh/publish_traits.tsv
[INFO] [2021-04-19 15:42:17] (2 lines) /app/public/data/tshudy_et_al_tsh/publish_metadata.tsv
[STOP] [2021-04-19 15:42:17] complete_harvest_instance
[START] [2021-04-19 15:42:17] completed
[STOP] [2021-04-19 15:42:17] completed
[STOP] [2021-04-19 15:42:17] logged process, took 102.95
Latest Process