Harvest for
Danielopol 1990
Created
19 Apr 14:58
Stage:
completed
Fetched:
19 Apr 14:58
Validated:
19 Apr 14:58
Deltas Created
19 Apr 14:58
Units Normalized:
19 Apr 14:58
Ancestry Built:
19 Apr 14:58
Nodes Matched:
19 Apr 14:58
Names Parsed:
19 Apr 14:58
New Models Stored:
19 Apr 14:58
Indexed:
19 Apr 14:58
Completed:
19 Apr 15:00
Time to Harvest:
less than a minute
Harvesting Log
(532 lines)
# Logfile created on 2020-08-27 15:24:13 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:24:13] logged process
[START] [2020-08-27 15:24:13] Creating resource from OpenData
[START] [2020-08-27 15:24:13] logged process
[START] [2020-08-27 15:24:13] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:24:13] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:24:13] Creating resource from OpenData
[INFO] [2020-11-19 13:39:28] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 13:39:32] ## remove_type: ScientificName
[INFO] [2020-11-19 13:39:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:39:32] [13:39:32.262] Removed 0 Scientificnames
[INFO] [2020-11-19 13:39:32] ## remove_type: Vernacular
[INFO] [2020-11-19 13:39:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:39:32] [13:39:32.264] Removed 0 Vernaculars
[INFO] [2020-11-19 13:39:32] ## remove_type: Article
[INFO] [2020-11-19 13:39:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:39:32] [13:39:32.267] Removed 0 Articles
[INFO] [2020-11-19 13:39:32] ## remove_type: Medium
[INFO] [2020-11-19 13:39:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:39:32] [13:39:32.270] Removed 0 Media
[INFO] [2020-11-19 13:39:32] ## remove_type: Trait
[INFO] [2020-11-19 13:39:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:39:32] [13:39:32.272] Removed 0 Traits
[INFO] [2020-11-19 13:39:32] ## remove_type: MetaTrait
[INFO] [2020-11-19 13:39:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:39:32] [13:39:32.275] Removed 0 Metatraits
[INFO] [2020-11-19 13:39:32] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 13:39:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:39:32] [13:39:32.277] Removed 0 Occurrencemetadata
[INFO] [2020-11-19 13:39:32] ## remove_type: Assoc
[INFO] [2020-11-19 13:39:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:39:32] [13:39:32.279] Removed 0 Assocs
[INFO] [2020-11-19 13:39:32] ## remove_type: MetaAssoc
[INFO] [2020-11-19 13:39:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:39:32] [13:39:32.281] Removed 0 Metaassocs
[INFO] [2020-11-19 13:39:32] ## remove_type: Identifier
[INFO] [2020-11-19 13:39:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:39:32] [13:39:32.284] Removed 0 Identifiers
[INFO] [2020-11-19 13:39:32] ## remove_type: Reference
[INFO] [2020-11-19 13:39:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:39:32] [13:39:32.286] Removed 0 References
[INFO] [2020-11-19 13:39:32] ## remove_type: Node
[INFO] [2020-11-19 13:39:32] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:39:32] [13:39:32.306] Removed 0 Nodes
[START] [2020-11-19 13:39:32] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 13:39:32] Creating resource from OpenData
[START] [2020-11-19 13:39:32] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 13:39:32] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:39:32] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:39:32] Creating resource from OpenData
[START] [2020-11-19 13:39:32] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-11-19 13:39:32] create_harvest_instance
[STOP] [2020-11-19 13:39:34] create_harvest_instance
[START] [2020-11-19 13:39:34] fetch_files
[STOP] [2020-11-19 13:39:34] fetch_files
[START] [2020-11-19 13:39:34] validate_each_file
[STOP] [2020-11-19 13:39:34] validate_each_file
[START] [2020-11-19 13:39:34] convert_to_csv
[CMD] [2020-11-19 13:39:34] /usr/bin/sort /app/public/converted_csv/danielopol_danie_refs_24438.csv > /app/public/converted_csv/danielopol_danie_refs_24438.csv_sorted
[CMD] [2020-11-19 13:39:34] /usr/bin/sort /app/public/converted_csv/danielopol_danie_nodes_24439.csv > /app/public/converted_csv/danielopol_danie_nodes_24439.csv_sorted
[CMD] [2020-11-19 13:39:34] /usr/bin/sort /app/public/converted_csv/danielopol_danie_occurrences_24440.csv > /app/public/converted_csv/danielopol_danie_occurrences_24440.csv_sorted
[CMD] [2020-11-19 13:39:34] /usr/bin/sort /app/public/converted_csv/danielopol_danie_measurements_24441.csv > /app/public/converted_csv/danielopol_danie_measurements_24441.csv_sorted
[STOP] [2020-11-19 13:39:34] convert_to_csv
[START] [2020-11-19 13:39:34] calculate_delta
[CMD] [2020-11-19 13:39:34] echo "0a" > /app/public/diff/danielopol_danie_refs_24438.diff
[CMD] [2020-11-19 13:39:34] tail -n +1 /app/public/converted_csv/danielopol_danie_refs_24438.csv >> /app/public/diff/danielopol_danie_refs_24438.diff
[CMD] [2020-11-19 13:39:34] echo "." >> /app/public/diff/danielopol_danie_refs_24438.diff
[CMD] [2020-11-19 13:39:34] echo "0a" > /app/public/diff/danielopol_danie_nodes_24439.diff
[CMD] [2020-11-19 13:39:34] tail -n +1 /app/public/converted_csv/danielopol_danie_nodes_24439.csv >> /app/public/diff/danielopol_danie_nodes_24439.diff
[CMD] [2020-11-19 13:39:34] echo "." >> /app/public/diff/danielopol_danie_nodes_24439.diff
[CMD] [2020-11-19 13:39:34] echo "0a" > /app/public/diff/danielopol_danie_occurrences_24440.diff
[CMD] [2020-11-19 13:39:34] tail -n +1 /app/public/converted_csv/danielopol_danie_occurrences_24440.csv >> /app/public/diff/danielopol_danie_occurrences_24440.diff
[CMD] [2020-11-19 13:39:34] echo "." >> /app/public/diff/danielopol_danie_occurrences_24440.diff
[CMD] [2020-11-19 13:39:34] echo "0a" > /app/public/diff/danielopol_danie_measurements_24441.diff
[CMD] [2020-11-19 13:39:34] tail -n +1 /app/public/converted_csv/danielopol_danie_measurements_24441.csv >> /app/public/diff/danielopol_danie_measurements_24441.diff
[CMD] [2020-11-19 13:39:34] echo "." >> /app/public/diff/danielopol_danie_measurements_24441.diff
[STOP] [2020-11-19 13:39:34] calculate_delta
[START] [2020-11-19 13:39:34] parse_diff_and_store
[INFO] [2020-11-19 13:39:34] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 13:39:34] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 13:39:34] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 13:39:34] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-19 13:39:35] Storing 1 ScientificNames
[INFO] [2020-11-19 13:39:35] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:39:35] Average Time: 0.0
[INFO] [2020-11-19 13:39:35] Total Time: 1s
[INFO] [2020-11-19 13:39:35] Storing 1 Nodes
[INFO] [2020-11-19 13:39:35] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:39:35] Average Time: 0.01
[INFO] [2020-11-19 13:39:35] Total Time: 1s
[INFO] [2020-11-19 13:39:35] Storing 1 Occurrences
[INFO] [2020-11-19 13:39:35] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:39:35] Average Time: 0.0
[INFO] [2020-11-19 13:39:35] Total Time: 1s
[INFO] [2020-11-19 13:39:35] Storing 2 Traits
[INFO] [2020-11-19 13:39:35] Processing group of 2 in 1 groups of 1000
[INFO] [2020-11-19 13:39:35] Average Time: 0.0
[INFO] [2020-11-19 13:39:35] Total Time: 1s
[INFO] [2020-11-19 13:39:35] Storing 1 MetaTraits
[INFO] [2020-11-19 13:39:35] Processing group of 1 in 1 groups of 1000
[INFO] [2020-11-19 13:39:35] Average Time: 0.0
[INFO] [2020-11-19 13:39:35] Total Time: 1s
[STOP] [2020-11-19 13:39:35] parse_diff_and_store
[START] [2020-11-19 13:39:35] resolve_keys
[INFO] [2020-11-19 13:39:41] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-19 13:39:41] traits to occurrences...
[INFO] [2020-11-19 13:39:41] traits to nodes (through occurrences)...
[INFO] [2020-11-19 13:39:41] Traits to sex term...
[INFO] [2020-11-19 13:39:41] Traits to lifestage term...
[INFO] [2020-11-19 13:39:41] MetaTraits to traits...
[INFO] [2020-11-19 13:39:41] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-19 13:39:41] Assocs to occurrences...
[INFO] [2020-11-19 13:39:41] Assocs to nodes...
[INFO] [2020-11-19 13:39:41] Assoc to sex term...
[INFO] [2020-11-19 13:39:41] Assoc to lifestage term...
[INFO] [2020-11-19 13:39:41] MetaAssoc to assocs...
[STOP] [2020-11-19 13:39:41] resolve_keys
[START] [2020-11-19 13:39:41] hold_for_later_1
[STOP] [2020-11-19 13:39:41] hold_for_later_1
[START] [2020-11-19 13:39:41] hold_for_later_2
[STOP] [2020-11-19 13:39:41] hold_for_later_2
[START] [2020-11-19 13:39:41] resolve_missing_parents
[STOP] [2020-11-19 13:39:41] resolve_missing_parents
[START] [2020-11-19 13:39:41] rebuild_nodes
[START] [2020-11-19 13:39:41] Flattener#flatten
[START] [2020-11-19 13:39:41] Flattener#study_resource
[START] [2020-11-19 13:39:41] Flattener#build_ancestry
[STOP] [2020-11-19 13:39:41] Flattener#build_ancestry
[INFO] [2020-11-19 13:39:41] 1 ancestry keys
[START] [2020-11-19 13:39:41] build_node_ancestors
[INFO] [2020-11-19 13:39:41] old ancestors deleted.
[STOP] [2020-11-19 13:39:41] build_node_ancestors
[WARN] [2020-11-19 13:39:41] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-19 13:39:41] Flattener#flatten
[STOP] [2020-11-19 13:39:41] rebuild_nodes
[START] [2020-11-19 13:39:41] resolve_missing_media_owners
[STOP] [2020-11-19 13:39:41] resolve_missing_media_owners
[START] [2020-11-19 13:39:41] sanitize_media_verbatims
[STOP] [2020-11-19 13:39:41] sanitize_media_verbatims
[START] [2020-11-19 13:39:41] queue_downloads
[STOP] [2020-11-19 13:39:41] queue_downloads
[START] [2020-11-19 13:39:41] parse_names
[WARN] [2020-11-19 13:39:41] I see 1 names which still need to be parsed.
[STOP] [2020-11-19 13:39:42] parse_names
[START] [2020-11-19 13:39:42] denormalize_canonical_names_to_nodes
[STOP] [2020-11-19 13:39:42] denormalize_canonical_names_to_nodes
[START] [2020-11-19 13:39:42] match_nodes
[START] [2020-11-19 13:39:42] map_all_nodes_to_pages
[STOP] [2020-11-19 13:39:42] map_all_nodes_to_pages
[INFO] [2020-11-19 13:39:42] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-11-19 13:39:42] update_nodes
[STOP] [2020-11-19 13:39:42] update_nodes
[STOP] [2020-11-19 13:39:42] match_nodes
[START] [2020-11-19 13:39:42] reindex_search
[STOP] [2020-11-19 13:39:42] reindex_search
[START] [2020-11-19 13:39:42] normalize_units
[STOP] [2020-11-19 13:39:42] normalize_units
[START] [2020-11-19 13:39:42] calculate_statistics
[2020-11-19 13:39:42] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-19 13:39:42] calculate_statistics
[START] [2020-11-19 13:39:42] complete_harvest_instance
[START] [2020-11-19 13:39:42] overall_tsv_creation
[INFO] [2020-11-19 13:39:42] Processing group of 1 in 1 batches of 10000
[INFO] [2020-11-19 13:40:25] 1 Traits (unfiltered)...
[INFO] [2020-11-19 13:41:08] 1 Traits (filtered)...
[INFO] [2020-11-19 13:41:08] 0 Associations (filtered)...
[INFO] [2020-11-19 13:41:08] 2 metadata added.
[INFO] [2020-11-19 13:41:08] 0 metadata added.
[INFO] [2020-11-19 13:41:08] Average Time: 66.46
[INFO] [2020-11-19 13:41:08] Total Time: 1m26s
[STOP] [2020-11-19 13:41:08] overall_tsv_creation
[INFO] [2020-11-19 13:41:08] Done. Check your files:
[INFO] [2020-11-19 13:41:08] (1 lines) /app/public/data/danielopol_danie/publish_nodes.tsv
[INFO] [2020-11-19 13:41:08] (1 lines) /app/public/data/danielopol_danie/publish_scientific_names.tsv
[INFO] [2020-11-19 13:41:08] (2 lines) /app/public/data/danielopol_danie/publish_traits.tsv
[INFO] [2020-11-19 13:41:08] (3 lines) /app/public/data/danielopol_danie/publish_metadata.tsv
[STOP] [2020-11-19 13:41:08] complete_harvest_instance
[START] [2020-11-19 13:41:08] completed
[STOP] [2020-11-19 13:41:08] completed
[STOP] [2020-11-19 13:41:08] logged process, took 96.08
[INFO] [2021-04-19 14:52:09] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 14:58:41] ## remove_type: ScientificName
[INFO] [2021-04-19 14:58:41] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:58:41] [14:58:41.702] Removed 1 Scientificnames
[INFO] [2021-04-19 14:58:41] ## remove_type: Vernacular
[INFO] [2021-04-19 14:58:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:58:41] [14:58:41.703] Removed 0 Vernaculars
[INFO] [2021-04-19 14:58:41] ## remove_type: Article
[INFO] [2021-04-19 14:58:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:58:41] [14:58:41.705] Removed 0 Articles
[INFO] [2021-04-19 14:58:41] ## remove_type: Medium
[INFO] [2021-04-19 14:58:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:58:41] [14:58:41.706] Removed 0 Media
[INFO] [2021-04-19 14:58:41] ## remove_type: Trait
[INFO] [2021-04-19 14:58:41] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 14:58:41] [14:58:41.708] Removed 2 Traits
[INFO] [2021-04-19 14:58:41] ## remove_type: MetaTrait
[INFO] [2021-04-19 14:58:41] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:58:41] [14:58:41.710] Removed 1 Metatraits
[INFO] [2021-04-19 14:58:41] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 14:58:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:58:41] [14:58:41.711] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 14:58:41] ## remove_type: Assoc
[INFO] [2021-04-19 14:58:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:58:41] [14:58:41.713] Removed 0 Assocs
[INFO] [2021-04-19 14:58:41] ## remove_type: MetaAssoc
[INFO] [2021-04-19 14:58:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:58:41] [14:58:41.714] Removed 0 Metaassocs
[INFO] [2021-04-19 14:58:41] ## remove_type: Identifier
[INFO] [2021-04-19 14:58:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:58:41] [14:58:41.716] Removed 0 Identifiers
[INFO] [2021-04-19 14:58:41] ## remove_type: Reference
[INFO] [2021-04-19 14:58:41] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 14:58:41] [14:58:41.717] Removed 0 References
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:41] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] Starting batch with ID 84620782...
[INFO] [2021-04-19 14:58:42] ## remove_type: Node
[INFO] [2021-04-19 14:58:42] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-19 14:58:42] [14:58:42.722] Removed 1 Nodes
[START] [2021-04-19 14:58:42] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:58:42] Creating resource from OpenData
[START] [2021-04-19 14:58:43] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:58:43] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 14:58:43] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 14:58:43] Creating resource from OpenData
[START] [2021-04-19 14:58:43] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 14:58:43] create_harvest_instance
[INFO] [2021-04-19 14:58:43] Created harvest instance #3756
[STOP] [2021-04-19 14:58:43] create_harvest_instance
[START] [2021-04-19 14:58:43] fetch_files
[STOP] [2021-04-19 14:58:43] fetch_files
[START] [2021-04-19 14:58:43] validate_each_file
[INFO] [2021-04-19 14:58:43] Looping over 4 formats...
[INFO] [2021-04-19 14:58:43] ...refs (/app/public/data/danielopol_danie/references.tsv)
[INFO] [2021-04-19 14:58:43] Valid: /app/public/converted_csv/danielopol_danie_refs_3756.csv (0 lines)
[INFO] [2021-04-19 14:58:43] ...nodes (/app/public/data/danielopol_danie/taxa.txt)
[INFO] [2021-04-19 14:58:43] Valid: /app/public/converted_csv/danielopol_danie_nodes_3756.csv (1 lines)
[INFO] [2021-04-19 14:58:43] ...occurrences (/app/public/data/danielopol_danie/occurrences.txt)
[INFO] [2021-04-19 14:58:43] Valid: /app/public/converted_csv/danielopol_danie_occurrences_3756.csv (1 lines)
[INFO] [2021-04-19 14:58:43] ...measurements (/app/public/data/danielopol_danie/measurementsorfacts.txt)
[INFO] [2021-04-19 14:58:43] Valid: /app/public/converted_csv/danielopol_danie_measurements_3756.csv (2 lines)
[STOP] [2021-04-19 14:58:43] validate_each_file
[START] [2021-04-19 14:58:43] convert_to_csv
[INFO] [2021-04-19 14:58:43] Looping over 4 formats...
[INFO] [2021-04-19 14:58:43] ...refs (/app/public/data/danielopol_danie/references.tsv)
[CMD] [2021-04-19 14:58:43] /usr/bin/sort /app/public/converted_csv/danielopol_danie_refs_3756.csv > /app/public/converted_csv/danielopol_danie_refs_3756.csv_sorted
[INFO] [2021-04-19 14:58:43] Converted: /app/public/converted_csv/danielopol_danie_refs_3756.csv (0 lines)
[INFO] [2021-04-19 14:58:43] ...nodes (/app/public/data/danielopol_danie/taxa.txt)
[CMD] [2021-04-19 14:58:43] /usr/bin/sort /app/public/converted_csv/danielopol_danie_nodes_3756.csv > /app/public/converted_csv/danielopol_danie_nodes_3756.csv_sorted
[INFO] [2021-04-19 14:58:43] Converted: /app/public/converted_csv/danielopol_danie_nodes_3756.csv (1 lines)
[INFO] [2021-04-19 14:58:43] ...occurrences (/app/public/data/danielopol_danie/occurrences.txt)
[CMD] [2021-04-19 14:58:43] /usr/bin/sort /app/public/converted_csv/danielopol_danie_occurrences_3756.csv > /app/public/converted_csv/danielopol_danie_occurrences_3756.csv_sorted
[INFO] [2021-04-19 14:58:43] Converted: /app/public/converted_csv/danielopol_danie_occurrences_3756.csv (1 lines)
[INFO] [2021-04-19 14:58:43] ...measurements (/app/public/data/danielopol_danie/measurementsorfacts.txt)
[CMD] [2021-04-19 14:58:43] /usr/bin/sort /app/public/converted_csv/danielopol_danie_measurements_3756.csv > /app/public/converted_csv/danielopol_danie_measurements_3756.csv_sorted
[INFO] [2021-04-19 14:58:43] Converted: /app/public/converted_csv/danielopol_danie_measurements_3756.csv (2 lines)
[STOP] [2021-04-19 14:58:43] convert_to_csv
[START] [2021-04-19 14:58:43] calculate_delta
[INFO] [2021-04-19 14:58:43] Looping over 4 formats...
[INFO] [2021-04-19 14:58:43] ...refs (/app/public/data/danielopol_danie/references.tsv)
[CMD] [2021-04-19 14:58:43] echo "0a" > /app/public/diff/danielopol_danie_refs_3756.diff
[CMD] [2021-04-19 14:58:43] tail -n +1 /app/public/converted_csv/danielopol_danie_refs_3756.csv >> /app/public/diff/danielopol_danie_refs_3756.diff
[CMD] [2021-04-19 14:58:43] echo "." >> /app/public/diff/danielopol_danie_refs_3756.diff
[INFO] [2021-04-19 14:58:43] Created diff: /app/public/diff/danielopol_danie_refs_3756.diff (2 lines)
[INFO] [2021-04-19 14:58:43] ...nodes (/app/public/data/danielopol_danie/taxa.txt)
[CMD] [2021-04-19 14:58:43] echo "0a" > /app/public/diff/danielopol_danie_nodes_3756.diff
[CMD] [2021-04-19 14:58:43] tail -n +1 /app/public/converted_csv/danielopol_danie_nodes_3756.csv >> /app/public/diff/danielopol_danie_nodes_3756.diff
[CMD] [2021-04-19 14:58:43] echo "." >> /app/public/diff/danielopol_danie_nodes_3756.diff
[INFO] [2021-04-19 14:58:43] Created diff: /app/public/diff/danielopol_danie_nodes_3756.diff (3 lines)
[INFO] [2021-04-19 14:58:43] ...occurrences (/app/public/data/danielopol_danie/occurrences.txt)
[CMD] [2021-04-19 14:58:43] echo "0a" > /app/public/diff/danielopol_danie_occurrences_3756.diff
[CMD] [2021-04-19 14:58:43] tail -n +1 /app/public/converted_csv/danielopol_danie_occurrences_3756.csv >> /app/public/diff/danielopol_danie_occurrences_3756.diff
[CMD] [2021-04-19 14:58:43] echo "." >> /app/public/diff/danielopol_danie_occurrences_3756.diff
[INFO] [2021-04-19 14:58:43] Created diff: /app/public/diff/danielopol_danie_occurrences_3756.diff (3 lines)
[INFO] [2021-04-19 14:58:43] ...measurements (/app/public/data/danielopol_danie/measurementsorfacts.txt)
[CMD] [2021-04-19 14:58:43] echo "0a" > /app/public/diff/danielopol_danie_measurements_3756.diff
[CMD] [2021-04-19 14:58:43] tail -n +1 /app/public/converted_csv/danielopol_danie_measurements_3756.csv >> /app/public/diff/danielopol_danie_measurements_3756.diff
[CMD] [2021-04-19 14:58:43] echo "." >> /app/public/diff/danielopol_danie_measurements_3756.diff
[INFO] [2021-04-19 14:58:43] Created diff: /app/public/diff/danielopol_danie_measurements_3756.diff (4 lines)
[STOP] [2021-04-19 14:58:43] calculate_delta
[START] [2021-04-19 14:58:43] parse_diff_and_store
[INFO] [2021-04-19 14:58:43] Handling diff: /app/public/diff/danielopol_danie_refs_3756.diff (2 lines)
[INFO] [2021-04-19 14:58:43] Loading refs diff file into memory (2 /app/public/diff/danielopol_danie_refs_3756.diff lines)...
[INFO] [2021-04-19 14:58:43] Handling diff: /app/public/diff/danielopol_danie_nodes_3756.diff (3 lines)
[INFO] [2021-04-19 14:58:43] Loading nodes diff file into memory (3 /app/public/diff/danielopol_danie_nodes_3756.diff lines)...
[INFO] [2021-04-19 14:58:43] Handling diff: /app/public/diff/danielopol_danie_occurrences_3756.diff (3 lines)
[INFO] [2021-04-19 14:58:43] Loading occurrences diff file into memory (3 /app/public/diff/danielopol_danie_occurrences_3756.diff lines)...
[INFO] [2021-04-19 14:58:43] Handling diff: /app/public/diff/danielopol_danie_measurements_3756.diff (4 lines)
[INFO] [2021-04-19 14:58:43] Loading measurements diff file into memory (4 /app/public/diff/danielopol_danie_measurements_3756.diff lines)...
[INFO] [2021-04-19 14:58:43] Storing 1 ScientificNames
[INFO] [2021-04-19 14:58:43] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:58:43] Average Time: 0.0
[INFO] [2021-04-19 14:58:43] Total Time: 1s
[INFO] [2021-04-19 14:58:43] Storing 1 Nodes
[INFO] [2021-04-19 14:58:43] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:58:43] Average Time: 0.0
[INFO] [2021-04-19 14:58:43] Total Time: 1s
[INFO] [2021-04-19 14:58:43] Storing 1 Occurrences
[INFO] [2021-04-19 14:58:43] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:58:43] Average Time: 0.0
[INFO] [2021-04-19 14:58:43] Total Time: 1s
[INFO] [2021-04-19 14:58:43] Storing 2 Traits
[INFO] [2021-04-19 14:58:43] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 14:58:43] Average Time: 0.0
[INFO] [2021-04-19 14:58:43] Total Time: 1s
[INFO] [2021-04-19 14:58:43] Storing 1 MetaTraits
[INFO] [2021-04-19 14:58:43] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-19 14:58:43] Average Time: 0.0
[INFO] [2021-04-19 14:58:43] Total Time: 1s
[STOP] [2021-04-19 14:58:43] parse_diff_and_store
[START] [2021-04-19 14:58:43] resolve_keys
[INFO] [2021-04-19 14:58:49] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 14:58:49] traits to occurrences...
[INFO] [2021-04-19 14:58:49] traits to nodes (through occurrences)...
[INFO] [2021-04-19 14:58:49] Traits to sex term...
[INFO] [2021-04-19 14:58:49] Traits to lifestage term...
[INFO] [2021-04-19 14:58:49] MetaTraits to traits...
[INFO] [2021-04-19 14:58:49] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 14:58:49] Assocs to occurrences...
[INFO] [2021-04-19 14:58:49] Assocs to nodes...
[INFO] [2021-04-19 14:58:49] Assoc to sex term...
[INFO] [2021-04-19 14:58:49] Assoc to lifestage term...
[INFO] [2021-04-19 14:58:49] MetaAssoc to assocs...
[STOP] [2021-04-19 14:58:49] resolve_keys
[START] [2021-04-19 14:58:49] hold_for_later_1
[STOP] [2021-04-19 14:58:49] hold_for_later_1
[START] [2021-04-19 14:58:49] hold_for_later_2
[STOP] [2021-04-19 14:58:49] hold_for_later_2
[START] [2021-04-19 14:58:49] resolve_missing_parents
[STOP] [2021-04-19 14:58:49] resolve_missing_parents
[START] [2021-04-19 14:58:49] rebuild_nodes
[START] [2021-04-19 14:58:49] Flattener#flatten
[START] [2021-04-19 14:58:49] Flattener#study_resource
[START] [2021-04-19 14:58:49] Flattener#build_ancestry
[STOP] [2021-04-19 14:58:49] Flattener#build_ancestry
[INFO] [2021-04-19 14:58:49] 1 ancestry keys
[START] [2021-04-19 14:58:49] build_node_ancestors
[INFO] [2021-04-19 14:58:49] old ancestors deleted.
[STOP] [2021-04-19 14:58:49] build_node_ancestors
[WARN] [2021-04-19 14:58:49] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 14:58:49] Flattener#flatten
[STOP] [2021-04-19 14:58:49] rebuild_nodes
[START] [2021-04-19 14:58:49] resolve_missing_media_owners
[STOP] [2021-04-19 14:58:49] resolve_missing_media_owners
[START] [2021-04-19 14:58:49] sanitize_media_verbatims
[STOP] [2021-04-19 14:58:49] sanitize_media_verbatims
[START] [2021-04-19 14:58:49] queue_downloads
[STOP] [2021-04-19 14:58:49] queue_downloads
[START] [2021-04-19 14:58:49] parse_names
[WARN] [2021-04-19 14:58:49] I see 1 names which still need to be parsed.
[STOP] [2021-04-19 14:58:50] parse_names
[START] [2021-04-19 14:58:50] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 14:58:50] denormalize_canonical_names_to_nodes
[START] [2021-04-19 14:58:50] match_nodes
[START] [2021-04-19 14:58:50] map_all_nodes_to_pages
[STOP] [2021-04-19 14:58:50] map_all_nodes_to_pages
[INFO] [2021-04-19 14:58:50] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2021-04-19 14:58:50] update_nodes
[STOP] [2021-04-19 14:58:50] update_nodes
[STOP] [2021-04-19 14:58:50] match_nodes
[START] [2021-04-19 14:58:50] reindex_search
[STOP] [2021-04-19 14:58:50] reindex_search
[START] [2021-04-19 14:58:50] normalize_units
[STOP] [2021-04-19 14:58:50] normalize_units
[START] [2021-04-19 14:58:50] calculate_statistics
[2021-04-19 14:58:50] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 14:58:50] calculate_statistics
[START] [2021-04-19 14:58:50] complete_harvest_instance
[START] [2021-04-19 14:58:50] overall_tsv_creation
[INFO] [2021-04-19 14:58:50] Processing group of 1 in 1 batches of 10000
[INFO] [2021-04-19 14:59:25] 1 Traits (unfiltered)...
[INFO] [2021-04-19 14:59:57] 1 Traits (filtered)...
[INFO] [2021-04-19 14:59:57] 0 Associations (filtered)...
[INFO] [2021-04-19 14:59:57] 1 metadata added.
[INFO] [2021-04-19 14:59:57] 0 metadata added.
[INFO] [2021-04-19 15:00:23] Average Time: 68.81
[INFO] [2021-04-19 15:00:23] Total Time: 1m33s
[STOP] [2021-04-19 15:00:23] overall_tsv_creation
[INFO] [2021-04-19 15:00:23] Done. Check your files:
[INFO] [2021-04-19 15:00:23] (1 lines) /app/public/data/danielopol_danie/publish_nodes.tsv
[INFO] [2021-04-19 15:00:23] (1 lines) /app/public/data/danielopol_danie/publish_scientific_names.tsv
[INFO] [2021-04-19 15:00:23] (2 lines) /app/public/data/danielopol_danie/publish_traits.tsv
[INFO] [2021-04-19 15:00:23] (2 lines) /app/public/data/danielopol_danie/publish_metadata.tsv
[STOP] [2021-04-19 15:00:23] complete_harvest_instance
[START] [2021-04-19 15:00:23] completed
[STOP] [2021-04-19 15:00:23] completed
[STOP] [2021-04-19 15:00:23] logged process, took 100.12
Latest Process