Stage:
completed
Fetched:
19 Apr 17:20
Validated:
19 Apr 17:20
Deltas Created
19 Apr 17:20
Units Normalized:
19 Apr 17:20
Ancestry Built:
19 Apr 17:20
Nodes Matched:
19 Apr 17:20
Names Parsed:
19 Apr 17:20
New Models Stored:
19 Apr 17:20
Indexed:
19 Apr 17:20
Completed:
19 Apr 17:22
Time to Harvest:
less than a minute
Harvesting Log
(480 lines)
# Logfile created on 2021-02-03 11:14:21 -0500 by logger.rb/v1.4.2
[START] [2021-02-03 11:14:21] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 11:14:21] Creating resource from OpenData
[START] [2021-02-03 11:14:21] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 11:14:21] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:14:21] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:14:21] Creating resource from OpenData
[INFO] [2021-02-03 11:16:41] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-02-03 11:16:43] ## remove_type: ScientificName
[INFO] [2021-02-03 11:16:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:16:43] [11:16:43.766] Removed 0 Scientificnames
[INFO] [2021-02-03 11:16:43] ## remove_type: Vernacular
[INFO] [2021-02-03 11:16:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:16:43] [11:16:43.768] Removed 0 Vernaculars
[INFO] [2021-02-03 11:16:43] ## remove_type: Article
[INFO] [2021-02-03 11:16:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:16:43] [11:16:43.771] Removed 0 Articles
[INFO] [2021-02-03 11:16:43] ## remove_type: Medium
[INFO] [2021-02-03 11:16:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:16:43] [11:16:43.774] Removed 0 Media
[INFO] [2021-02-03 11:16:43] ## remove_type: Trait
[INFO] [2021-02-03 11:16:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:16:43] [11:16:43.777] Removed 0 Traits
[INFO] [2021-02-03 11:16:43] ## remove_type: MetaTrait
[INFO] [2021-02-03 11:16:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:16:43] [11:16:43.780] Removed 0 Metatraits
[INFO] [2021-02-03 11:16:43] ## remove_type: OccurrenceMetadatum
[INFO] [2021-02-03 11:16:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:16:43] [11:16:43.783] Removed 0 Occurrencemetadata
[INFO] [2021-02-03 11:16:43] ## remove_type: Assoc
[INFO] [2021-02-03 11:16:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:16:43] [11:16:43.785] Removed 0 Assocs
[INFO] [2021-02-03 11:16:43] ## remove_type: MetaAssoc
[INFO] [2021-02-03 11:16:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:16:43] [11:16:43.788] Removed 0 Metaassocs
[INFO] [2021-02-03 11:16:43] ## remove_type: Identifier
[INFO] [2021-02-03 11:16:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:16:43] [11:16:43.791] Removed 0 Identifiers
[INFO] [2021-02-03 11:16:43] ## remove_type: Reference
[INFO] [2021-02-03 11:16:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:16:43] [11:16:43.793] Removed 0 References
[INFO] [2021-02-03 11:16:43] ## remove_type: Node
[INFO] [2021-02-03 11:16:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:16:43] [11:16:43.816] Removed 0 Nodes
[START] [2021-02-03 11:16:43] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 11:16:43] Creating resource from OpenData
[START] [2021-02-03 11:16:43] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 11:16:43] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:16:44] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:16:44] Creating resource from OpenData
[START] [2021-02-03 11:16:44] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 11:16:44] create_harvest_instance
[STOP] [2021-02-03 11:16:45] create_harvest_instance
[START] [2021-02-03 11:16:45] fetch_files
[STOP] [2021-02-03 11:16:45] fetch_files
[START] [2021-02-03 11:16:45] validate_each_file
[STOP] [2021-02-03 11:16:45] validate_each_file
[START] [2021-02-03 11:16:45] convert_to_csv
[CMD] [2021-02-03 11:16:45] /usr/bin/sort /app/public/converted_csv/wcislo_et_al_wci_nodes_26665.csv > /app/public/converted_csv/wcislo_et_al_wci_nodes_26665.csv_sorted
[CMD] [2021-02-03 11:16:45] /usr/bin/sort /app/public/converted_csv/wcislo_et_al_wci_occurrences_26666.csv > /app/public/converted_csv/wcislo_et_al_wci_occurrences_26666.csv_sorted
[CMD] [2021-02-03 11:16:45] /usr/bin/sort /app/public/converted_csv/wcislo_et_al_wci_measurements_26667.csv > /app/public/converted_csv/wcislo_et_al_wci_measurements_26667.csv_sorted
[STOP] [2021-02-03 11:16:45] convert_to_csv
[START] [2021-02-03 11:16:45] calculate_delta
[CMD] [2021-02-03 11:16:45] echo "0a" > /app/public/diff/wcislo_et_al_wci_nodes_26665.diff
[CMD] [2021-02-03 11:16:45] tail -n +1 /app/public/converted_csv/wcislo_et_al_wci_nodes_26665.csv >> /app/public/diff/wcislo_et_al_wci_nodes_26665.diff
[CMD] [2021-02-03 11:16:45] echo "." >> /app/public/diff/wcislo_et_al_wci_nodes_26665.diff
[CMD] [2021-02-03 11:16:45] echo "0a" > /app/public/diff/wcislo_et_al_wci_occurrences_26666.diff
[CMD] [2021-02-03 11:16:45] tail -n +1 /app/public/converted_csv/wcislo_et_al_wci_occurrences_26666.csv >> /app/public/diff/wcislo_et_al_wci_occurrences_26666.diff
[CMD] [2021-02-03 11:16:45] echo "." >> /app/public/diff/wcislo_et_al_wci_occurrences_26666.diff
[CMD] [2021-02-03 11:16:45] echo "0a" > /app/public/diff/wcislo_et_al_wci_measurements_26667.diff
[CMD] [2021-02-03 11:16:45] tail -n +1 /app/public/converted_csv/wcislo_et_al_wci_measurements_26667.csv >> /app/public/diff/wcislo_et_al_wci_measurements_26667.diff
[CMD] [2021-02-03 11:16:45] echo "." >> /app/public/diff/wcislo_et_al_wci_measurements_26667.diff
[STOP] [2021-02-03 11:16:45] calculate_delta
[START] [2021-02-03 11:16:45] parse_diff_and_store
[INFO] [2021-02-03 11:16:45] Loading nodes diff file into memory (true lines)...
[INFO] [2021-02-03 11:16:46] Loading occurrences diff file into memory (true lines)...
[INFO] [2021-02-03 11:16:46] Loading measurements diff file into memory (true lines)...
[INFO] [2021-02-03 11:16:46] Storing 5 ScientificNames
[INFO] [2021-02-03 11:16:46] Processing group of 5 in 1 groups of 1000
[INFO] [2021-02-03 11:16:46] Average Time: 0.0
[INFO] [2021-02-03 11:16:46] Total Time: 1s
[INFO] [2021-02-03 11:16:46] Storing 5 Nodes
[INFO] [2021-02-03 11:16:46] Processing group of 5 in 1 groups of 1000
[INFO] [2021-02-03 11:16:46] Average Time: 0.0
[INFO] [2021-02-03 11:16:46] Total Time: 1s
[INFO] [2021-02-03 11:16:46] Storing 2 Occurrences
[INFO] [2021-02-03 11:16:46] Processing group of 2 in 1 groups of 1000
[INFO] [2021-02-03 11:16:46] Average Time: 0.01
[INFO] [2021-02-03 11:16:46] Total Time: 1s
[INFO] [2021-02-03 11:16:46] Storing 2 OccurrenceMetadata
[INFO] [2021-02-03 11:16:46] Processing group of 2 in 1 groups of 1000
[INFO] [2021-02-03 11:16:46] Average Time: 0.0
[INFO] [2021-02-03 11:16:46] Total Time: 1s
[INFO] [2021-02-03 11:16:46] Storing 2 Traits
[INFO] [2021-02-03 11:16:46] Processing group of 2 in 1 groups of 1000
[INFO] [2021-02-03 11:16:47] Average Time: 0.0
[INFO] [2021-02-03 11:16:47] Total Time: 1s
[INFO] [2021-02-03 11:16:47] Storing 2 MetaTraits
[INFO] [2021-02-03 11:16:47] Processing group of 2 in 1 groups of 1000
[INFO] [2021-02-03 11:16:47] Average Time: 0.0
[INFO] [2021-02-03 11:16:47] Total Time: 1s
[STOP] [2021-02-03 11:16:47] parse_diff_and_store
[START] [2021-02-03 11:16:47] resolve_keys
[INFO] [2021-02-03 11:16:52] Occurrences to nodes (through scientific_names)...
[INFO] [2021-02-03 11:16:52] traits to occurrences...
[INFO] [2021-02-03 11:16:52] traits to nodes (through occurrences)...
[INFO] [2021-02-03 11:16:52] Traits to sex term...
[INFO] [2021-02-03 11:16:52] Traits to lifestage term...
[INFO] [2021-02-03 11:16:52] MetaTraits to traits...
[INFO] [2021-02-03 11:16:52] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-02-03 11:16:52] Assocs to occurrences...
[INFO] [2021-02-03 11:16:52] Assocs to nodes...
[INFO] [2021-02-03 11:16:52] Assoc to sex term...
[INFO] [2021-02-03 11:16:52] Assoc to lifestage term...
[INFO] [2021-02-03 11:16:52] MetaAssoc to assocs...
[STOP] [2021-02-03 11:16:52] resolve_keys
[START] [2021-02-03 11:16:52] hold_for_later_1
[STOP] [2021-02-03 11:16:52] hold_for_later_1
[START] [2021-02-03 11:16:52] hold_for_later_2
[STOP] [2021-02-03 11:16:52] hold_for_later_2
[START] [2021-02-03 11:16:52] resolve_missing_parents
[STOP] [2021-02-03 11:16:52] resolve_missing_parents
[START] [2021-02-03 11:16:52] rebuild_nodes
[START] [2021-02-03 11:16:52] Flattener#flatten
[START] [2021-02-03 11:16:52] Flattener#study_resource
[START] [2021-02-03 11:16:52] Flattener#build_ancestry
[STOP] [2021-02-03 11:16:52] Flattener#build_ancestry
[INFO] [2021-02-03 11:16:52] 5 ancestry keys
[START] [2021-02-03 11:16:52] build_node_ancestors
[INFO] [2021-02-03 11:16:52] old ancestors deleted.
[STOP] [2021-02-03 11:16:52] build_node_ancestors
[START] [2021-02-03 11:16:52] Flattener#propagate_ancestor_ids
[STOP] [2021-02-03 11:16:52] Flattener#propagate_ancestor_ids
[STOP] [2021-02-03 11:16:52] Flattener#flatten
[STOP] [2021-02-03 11:16:52] rebuild_nodes
[START] [2021-02-03 11:16:52] resolve_missing_media_owners
[STOP] [2021-02-03 11:16:52] resolve_missing_media_owners
[START] [2021-02-03 11:16:52] sanitize_media_verbatims
[STOP] [2021-02-03 11:16:52] sanitize_media_verbatims
[START] [2021-02-03 11:16:52] queue_downloads
[STOP] [2021-02-03 11:16:52] queue_downloads
[START] [2021-02-03 11:16:52] parse_names
[WARN] [2021-02-03 11:16:52] I see 5 names which still need to be parsed.
[STOP] [2021-02-03 11:16:53] parse_names
[START] [2021-02-03 11:16:53] denormalize_canonical_names_to_nodes
[STOP] [2021-02-03 11:16:53] denormalize_canonical_names_to_nodes
[START] [2021-02-03 11:16:53] match_nodes
[START] [2021-02-03 11:16:53] map_all_nodes_to_pages
[STOP] [2021-02-03 11:16:54] map_all_nodes_to_pages
[INFO] [2021-02-03 11:16:54] Unmatched nodes (1 of 5): Megalopta ecuadoria (#87728853)
[START] [2021-02-03 11:16:54] update_nodes
[STOP] [2021-02-03 11:16:54] update_nodes
[STOP] [2021-02-03 11:16:54] match_nodes
[START] [2021-02-03 11:16:54] reindex_search
[STOP] [2021-02-03 11:16:54] reindex_search
[START] [2021-02-03 11:16:54] normalize_units
[STOP] [2021-02-03 11:16:54] normalize_units
[START] [2021-02-03 11:16:54] calculate_statistics
[STOP] [2021-02-03 11:16:54] calculate_statistics
[START] [2021-02-03 11:16:54] complete_harvest_instance
[START] [2021-02-03 11:16:54] overall_tsv_creation
[INFO] [2021-02-03 11:16:54] Processing group of 5 in 1 batches of 10000
[INFO] [2021-02-03 11:17:33] 2 Traits (unfiltered)...
[INFO] [2021-02-03 11:18:12] 2 Traits (filtered)...
[INFO] [2021-02-03 11:18:12] 0 Associations (filtered)...
[INFO] [2021-02-03 11:18:12] 2 metadata added.
[INFO] [2021-02-03 11:18:12] 0 metadata added.
[INFO] [2021-02-03 11:18:46] Average Time: 86.29
[INFO] [2021-02-03 11:18:46] Total Time: 1m52s
[STOP] [2021-02-03 11:18:46] overall_tsv_creation
[INFO] [2021-02-03 11:18:46] Done. Check your files:
[INFO] [2021-02-03 11:18:46] (5 lines) /app/public/data/wcislo_et_al_wci/publish_nodes.tsv
[INFO] [2021-02-03 11:18:46] (6 lines) /app/public/data/wcislo_et_al_wci/publish_node_ancestors.tsv
[INFO] [2021-02-03 11:18:46] (5 lines) /app/public/data/wcislo_et_al_wci/publish_scientific_names.tsv
[INFO] [2021-02-03 11:18:46] (3 lines) /app/public/data/wcislo_et_al_wci/publish_traits.tsv
[INFO] [2021-02-03 11:18:46] (3 lines) /app/public/data/wcislo_et_al_wci/publish_metadata.tsv
[STOP] [2021-02-03 11:18:46] complete_harvest_instance
[START] [2021-02-03 11:18:46] completed
[STOP] [2021-02-03 11:18:46] completed
[STOP] [2021-02-03 11:18:46] logged process, took 122.62
[INFO] [2021-04-19 16:54:46] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 17:20:43] ## remove_type: ScientificName
[INFO] [2021-04-19 17:20:43] ++ Calling delete_all on 5 instances...
[INFO] [2021-04-19 17:20:43] [17:20:43.500] Removed 5 Scientificnames
[INFO] [2021-04-19 17:20:43] ## remove_type: Vernacular
[INFO] [2021-04-19 17:20:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:20:43] [17:20:43.502] Removed 0 Vernaculars
[INFO] [2021-04-19 17:20:43] ## remove_type: Article
[INFO] [2021-04-19 17:20:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:20:43] [17:20:43.503] Removed 0 Articles
[INFO] [2021-04-19 17:20:43] ## remove_type: Medium
[INFO] [2021-04-19 17:20:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:20:43] [17:20:43.505] Removed 0 Media
[INFO] [2021-04-19 17:20:43] ## remove_type: Trait
[INFO] [2021-04-19 17:20:43] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 17:20:43] [17:20:43.507] Removed 2 Traits
[INFO] [2021-04-19 17:20:43] ## remove_type: MetaTrait
[INFO] [2021-04-19 17:20:43] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 17:20:43] [17:20:43.509] Removed 2 Metatraits
[INFO] [2021-04-19 17:20:43] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 17:20:43] ++ Calling delete_all on 2 instances...
[INFO] [2021-04-19 17:20:43] [17:20:43.513] Removed 2 Occurrencemetadata
[INFO] [2021-04-19 17:20:43] ## remove_type: Assoc
[INFO] [2021-04-19 17:20:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:20:43] [17:20:43.514] Removed 0 Assocs
[INFO] [2021-04-19 17:20:43] ## remove_type: MetaAssoc
[INFO] [2021-04-19 17:20:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:20:43] [17:20:43.516] Removed 0 Metaassocs
[INFO] [2021-04-19 17:20:43] ## remove_type: Identifier
[INFO] [2021-04-19 17:20:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:20:43] [17:20:43.518] Removed 0 Identifiers
[INFO] [2021-04-19 17:20:43] ## remove_type: Reference
[INFO] [2021-04-19 17:20:43] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 17:20:43] [17:20:43.520] Removed 0 References
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:43] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728850...
[INFO] [2021-04-19 17:20:44] Starting batch with ID 87728854...
[INFO] [2021-04-19 17:20:44] ## remove_type: Node
[INFO] [2021-04-19 17:20:44] ++ Calling delete_all on 5 instances...
[INFO] [2021-04-19 17:20:44] [17:20:44.180] Removed 5 Nodes
[START] [2021-04-19 17:20:44] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:20:44] Creating resource from OpenData
[START] [2021-04-19 17:20:44] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:20:44] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 17:20:44] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 17:20:44] Creating resource from OpenData
[START] [2021-04-19 17:20:44] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 17:20:44] create_harvest_instance
[INFO] [2021-04-19 17:20:44] Created harvest instance #3824
[STOP] [2021-04-19 17:20:44] create_harvest_instance
[START] [2021-04-19 17:20:44] fetch_files
[STOP] [2021-04-19 17:20:44] fetch_files
[START] [2021-04-19 17:20:44] validate_each_file
[INFO] [2021-04-19 17:20:44] Looping over 3 formats...
[INFO] [2021-04-19 17:20:44] ...nodes (/app/public/data/wcislo_et_al_wci/taxa.txt)
[INFO] [2021-04-19 17:20:44] Valid: /app/public/converted_csv/wcislo_et_al_wci_nodes_3824.csv (2 lines)
[INFO] [2021-04-19 17:20:44] ...occurrences (/app/public/data/wcislo_et_al_wci/occurrences.txt)
[INFO] [2021-04-19 17:20:44] Valid: /app/public/converted_csv/wcislo_et_al_wci_occurrences_3824.csv (2 lines)
[INFO] [2021-04-19 17:20:44] ...measurements (/app/public/data/wcislo_et_al_wci/measurementsorfacts.txt)
[INFO] [2021-04-19 17:20:44] Valid: /app/public/converted_csv/wcislo_et_al_wci_measurements_3824.csv (2 lines)
[STOP] [2021-04-19 17:20:44] validate_each_file
[START] [2021-04-19 17:20:44] convert_to_csv
[INFO] [2021-04-19 17:20:44] Looping over 3 formats...
[INFO] [2021-04-19 17:20:44] ...nodes (/app/public/data/wcislo_et_al_wci/taxa.txt)
[CMD] [2021-04-19 17:20:44] /usr/bin/sort /app/public/converted_csv/wcislo_et_al_wci_nodes_3824.csv > /app/public/converted_csv/wcislo_et_al_wci_nodes_3824.csv_sorted
[INFO] [2021-04-19 17:20:44] Converted: /app/public/converted_csv/wcislo_et_al_wci_nodes_3824.csv (2 lines)
[INFO] [2021-04-19 17:20:44] ...occurrences (/app/public/data/wcislo_et_al_wci/occurrences.txt)
[CMD] [2021-04-19 17:20:44] /usr/bin/sort /app/public/converted_csv/wcislo_et_al_wci_occurrences_3824.csv > /app/public/converted_csv/wcislo_et_al_wci_occurrences_3824.csv_sorted
[INFO] [2021-04-19 17:20:44] Converted: /app/public/converted_csv/wcislo_et_al_wci_occurrences_3824.csv (2 lines)
[INFO] [2021-04-19 17:20:44] ...measurements (/app/public/data/wcislo_et_al_wci/measurementsorfacts.txt)
[CMD] [2021-04-19 17:20:44] /usr/bin/sort /app/public/converted_csv/wcislo_et_al_wci_measurements_3824.csv > /app/public/converted_csv/wcislo_et_al_wci_measurements_3824.csv_sorted
[INFO] [2021-04-19 17:20:44] Converted: /app/public/converted_csv/wcislo_et_al_wci_measurements_3824.csv (2 lines)
[STOP] [2021-04-19 17:20:44] convert_to_csv
[START] [2021-04-19 17:20:44] calculate_delta
[INFO] [2021-04-19 17:20:44] Looping over 3 formats...
[INFO] [2021-04-19 17:20:44] ...nodes (/app/public/data/wcislo_et_al_wci/taxa.txt)
[CMD] [2021-04-19 17:20:44] echo "0a" > /app/public/diff/wcislo_et_al_wci_nodes_3824.diff
[CMD] [2021-04-19 17:20:44] tail -n +1 /app/public/converted_csv/wcislo_et_al_wci_nodes_3824.csv >> /app/public/diff/wcislo_et_al_wci_nodes_3824.diff
[CMD] [2021-04-19 17:20:44] echo "." >> /app/public/diff/wcislo_et_al_wci_nodes_3824.diff
[INFO] [2021-04-19 17:20:44] Created diff: /app/public/diff/wcislo_et_al_wci_nodes_3824.diff (4 lines)
[INFO] [2021-04-19 17:20:44] ...occurrences (/app/public/data/wcislo_et_al_wci/occurrences.txt)
[CMD] [2021-04-19 17:20:44] echo "0a" > /app/public/diff/wcislo_et_al_wci_occurrences_3824.diff
[CMD] [2021-04-19 17:20:44] tail -n +1 /app/public/converted_csv/wcislo_et_al_wci_occurrences_3824.csv >> /app/public/diff/wcislo_et_al_wci_occurrences_3824.diff
[CMD] [2021-04-19 17:20:44] echo "." >> /app/public/diff/wcislo_et_al_wci_occurrences_3824.diff
[INFO] [2021-04-19 17:20:44] Created diff: /app/public/diff/wcislo_et_al_wci_occurrences_3824.diff (4 lines)
[INFO] [2021-04-19 17:20:44] ...measurements (/app/public/data/wcislo_et_al_wci/measurementsorfacts.txt)
[CMD] [2021-04-19 17:20:44] echo "0a" > /app/public/diff/wcislo_et_al_wci_measurements_3824.diff
[CMD] [2021-04-19 17:20:44] tail -n +1 /app/public/converted_csv/wcislo_et_al_wci_measurements_3824.csv >> /app/public/diff/wcislo_et_al_wci_measurements_3824.diff
[CMD] [2021-04-19 17:20:44] echo "." >> /app/public/diff/wcislo_et_al_wci_measurements_3824.diff
[INFO] [2021-04-19 17:20:44] Created diff: /app/public/diff/wcislo_et_al_wci_measurements_3824.diff (4 lines)
[STOP] [2021-04-19 17:20:44] calculate_delta
[START] [2021-04-19 17:20:44] parse_diff_and_store
[INFO] [2021-04-19 17:20:44] Handling diff: /app/public/diff/wcislo_et_al_wci_nodes_3824.diff (4 lines)
[INFO] [2021-04-19 17:20:44] Loading nodes diff file into memory (4 /app/public/diff/wcislo_et_al_wci_nodes_3824.diff lines)...
[INFO] [2021-04-19 17:20:44] Handling diff: /app/public/diff/wcislo_et_al_wci_occurrences_3824.diff (4 lines)
[INFO] [2021-04-19 17:20:44] Loading occurrences diff file into memory (4 /app/public/diff/wcislo_et_al_wci_occurrences_3824.diff lines)...
[INFO] [2021-04-19 17:20:44] Handling diff: /app/public/diff/wcislo_et_al_wci_measurements_3824.diff (4 lines)
[INFO] [2021-04-19 17:20:44] Loading measurements diff file into memory (4 /app/public/diff/wcislo_et_al_wci_measurements_3824.diff lines)...
[INFO] [2021-04-19 17:20:44] Storing 5 ScientificNames
[INFO] [2021-04-19 17:20:44] Processing group of 5 in 1 groups of 1000
[INFO] [2021-04-19 17:20:44] Average Time: 0.0
[INFO] [2021-04-19 17:20:44] Total Time: 1s
[INFO] [2021-04-19 17:20:44] Storing 5 Nodes
[INFO] [2021-04-19 17:20:44] Processing group of 5 in 1 groups of 1000
[INFO] [2021-04-19 17:20:44] Average Time: 0.0
[INFO] [2021-04-19 17:20:44] Total Time: 1s
[INFO] [2021-04-19 17:20:44] Storing 2 Occurrences
[INFO] [2021-04-19 17:20:44] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 17:20:44] Average Time: 0.0
[INFO] [2021-04-19 17:20:44] Total Time: 1s
[INFO] [2021-04-19 17:20:44] Storing 2 OccurrenceMetadata
[INFO] [2021-04-19 17:20:44] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 17:20:44] Average Time: 0.0
[INFO] [2021-04-19 17:20:44] Total Time: 1s
[INFO] [2021-04-19 17:20:44] Storing 2 Traits
[INFO] [2021-04-19 17:20:44] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 17:20:44] Average Time: 0.0
[INFO] [2021-04-19 17:20:44] Total Time: 1s
[INFO] [2021-04-19 17:20:44] Storing 2 MetaTraits
[INFO] [2021-04-19 17:20:44] Processing group of 2 in 1 groups of 1000
[INFO] [2021-04-19 17:20:44] Average Time: 0.0
[INFO] [2021-04-19 17:20:44] Total Time: 1s
[STOP] [2021-04-19 17:20:44] parse_diff_and_store
[START] [2021-04-19 17:20:44] resolve_keys
[INFO] [2021-04-19 17:20:50] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 17:20:50] traits to occurrences...
[INFO] [2021-04-19 17:20:50] traits to nodes (through occurrences)...
[INFO] [2021-04-19 17:20:50] Traits to sex term...
[INFO] [2021-04-19 17:20:50] Traits to lifestage term...
[INFO] [2021-04-19 17:20:50] MetaTraits to traits...
[INFO] [2021-04-19 17:20:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 17:20:50] Assocs to occurrences...
[INFO] [2021-04-19 17:20:50] Assocs to nodes...
[INFO] [2021-04-19 17:20:50] Assoc to sex term...
[INFO] [2021-04-19 17:20:50] Assoc to lifestage term...
[INFO] [2021-04-19 17:20:50] MetaAssoc to assocs...
[STOP] [2021-04-19 17:20:50] resolve_keys
[START] [2021-04-19 17:20:50] hold_for_later_1
[STOP] [2021-04-19 17:20:50] hold_for_later_1
[START] [2021-04-19 17:20:50] hold_for_later_2
[STOP] [2021-04-19 17:20:50] hold_for_later_2
[START] [2021-04-19 17:20:50] resolve_missing_parents
[STOP] [2021-04-19 17:20:50] resolve_missing_parents
[START] [2021-04-19 17:20:50] rebuild_nodes
[START] [2021-04-19 17:20:50] Flattener#flatten
[START] [2021-04-19 17:20:50] Flattener#study_resource
[START] [2021-04-19 17:20:50] Flattener#build_ancestry
[STOP] [2021-04-19 17:20:50] Flattener#build_ancestry
[INFO] [2021-04-19 17:20:50] 5 ancestry keys
[START] [2021-04-19 17:20:50] build_node_ancestors
[INFO] [2021-04-19 17:20:50] old ancestors deleted.
[STOP] [2021-04-19 17:20:50] build_node_ancestors
[START] [2021-04-19 17:20:50] Flattener#propagate_ancestor_ids
[STOP] [2021-04-19 17:20:50] Flattener#propagate_ancestor_ids
[STOP] [2021-04-19 17:20:50] Flattener#flatten
[STOP] [2021-04-19 17:20:50] rebuild_nodes
[START] [2021-04-19 17:20:50] resolve_missing_media_owners
[STOP] [2021-04-19 17:20:50] resolve_missing_media_owners
[START] [2021-04-19 17:20:50] sanitize_media_verbatims
[STOP] [2021-04-19 17:20:50] sanitize_media_verbatims
[START] [2021-04-19 17:20:50] queue_downloads
[STOP] [2021-04-19 17:20:50] queue_downloads
[START] [2021-04-19 17:20:50] parse_names
[WARN] [2021-04-19 17:20:50] I see 5 names which still need to be parsed.
[STOP] [2021-04-19 17:20:52] parse_names
[START] [2021-04-19 17:20:52] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 17:20:52] denormalize_canonical_names_to_nodes
[START] [2021-04-19 17:20:52] match_nodes
[START] [2021-04-19 17:20:52] map_all_nodes_to_pages
[STOP] [2021-04-19 17:20:52] map_all_nodes_to_pages
[INFO] [2021-04-19 17:20:52] Unmatched nodes (1 of 5): Megalopta ecuadoria (#92874520)
[START] [2021-04-19 17:20:52] update_nodes
[STOP] [2021-04-19 17:20:52] update_nodes
[STOP] [2021-04-19 17:20:52] match_nodes
[START] [2021-04-19 17:20:52] reindex_search
[STOP] [2021-04-19 17:20:52] reindex_search
[START] [2021-04-19 17:20:52] normalize_units
[STOP] [2021-04-19 17:20:52] normalize_units
[START] [2021-04-19 17:20:52] calculate_statistics
[STOP] [2021-04-19 17:20:52] calculate_statistics
[START] [2021-04-19 17:20:52] complete_harvest_instance
[START] [2021-04-19 17:20:52] overall_tsv_creation
[INFO] [2021-04-19 17:20:52] Processing group of 5 in 1 batches of 10000
[INFO] [2021-04-19 17:21:28] 2 Traits (unfiltered)...
[INFO] [2021-04-19 17:22:02] 2 Traits (filtered)...
[INFO] [2021-04-19 17:22:02] 0 Associations (filtered)...
[INFO] [2021-04-19 17:22:02] 0 metadata added.
[INFO] [2021-04-19 17:22:02] 0 metadata added.
[INFO] [2021-04-19 17:22:28] Average Time: 72.46
[INFO] [2021-04-19 17:22:28] Total Time: 1m37s
[STOP] [2021-04-19 17:22:28] overall_tsv_creation
[INFO] [2021-04-19 17:22:28] Done. Check your files:
[INFO] [2021-04-19 17:22:28] (5 lines) /app/public/data/wcislo_et_al_wci/publish_nodes.tsv
[INFO] [2021-04-19 17:22:28] (6 lines) /app/public/data/wcislo_et_al_wci/publish_node_ancestors.tsv
[INFO] [2021-04-19 17:22:28] (5 lines) /app/public/data/wcislo_et_al_wci/publish_scientific_names.tsv
[INFO] [2021-04-19 17:22:28] (3 lines) /app/public/data/wcislo_et_al_wci/publish_traits.tsv
[INFO] [2021-04-19 17:22:28] (1 lines) /app/public/data/wcislo_et_al_wci/publish_metadata.tsv
[STOP] [2021-04-19 17:22:28] complete_harvest_instance
[START] [2021-04-19 17:22:28] completed
[STOP] [2021-04-19 17:22:28] completed
[STOP] [2021-04-19 17:22:28] logged process, took 104.39
Latest Process