Harvest for Maddison et al 2019 Created 19 Apr 09:41

Harvesting Log

# Logfile created on 2020-08-27 15:19:35 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:19:35] logged process
[START] [2020-08-27 15:19:35] Creating resource from OpenData
[START] [2020-08-27 15:19:36] logged process
[START] [2020-08-27 15:19:36] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:19:36] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:19:36] Creating resource from OpenData
[INFO] [2020-11-19 12:40:44] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 12:40:46] ## remove_type: ScientificName
[INFO] [2020-11-19 12:40:46] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:40:46] [12:40:46.355] Removed 0 Scientificnames
[INFO] [2020-11-19 12:40:46] ## remove_type: Vernacular
[INFO] [2020-11-19 12:40:46] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:40:46] [12:40:46.361] Removed 0 Vernaculars
[INFO] [2020-11-19 12:40:46] ## remove_type: Article
[INFO] [2020-11-19 12:40:46] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:40:46] [12:40:46.364] Removed 0 Articles
[INFO] [2020-11-19 12:40:46] ## remove_type: Medium
[INFO] [2020-11-19 12:40:46] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:40:46] [12:40:46.368] Removed 0 Media
[INFO] [2020-11-19 12:40:46] ## remove_type: Trait
[INFO] [2020-11-19 12:40:46] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:40:46] [12:40:46.371] Removed 0 Traits
[INFO] [2020-11-19 12:40:46] ## remove_type: MetaTrait
[INFO] [2020-11-19 12:40:46] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:40:46] [12:40:46.377] Removed 0 Metatraits
[INFO] [2020-11-19 12:40:46] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 12:40:46] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:40:46] [12:40:46.380] Removed 0 Occurrencemetadata
[INFO] [2020-11-19 12:40:46] ## remove_type: Assoc
[INFO] [2020-11-19 12:40:46] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:40:46] [12:40:46.387] Removed 0 Assocs
[INFO] [2020-11-19 12:40:46] ## remove_type: MetaAssoc
[INFO] [2020-11-19 12:40:46] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:40:46] [12:40:46.390] Removed 0 Metaassocs
[INFO] [2020-11-19 12:40:46] ## remove_type: Identifier
[INFO] [2020-11-19 12:40:46] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:40:46] [12:40:46.392] Removed 0 Identifiers
[INFO] [2020-11-19 12:40:46] ## remove_type: Reference
[INFO] [2020-11-19 12:40:46] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:40:46] [12:40:46.395] Removed 0 References
[INFO] [2020-11-19 12:40:46] ## remove_type: Node
[INFO] [2020-11-19 12:40:46] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 12:40:46] [12:40:46.417] Removed 0 Nodes
[START] [2020-11-19 12:40:46] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 12:40:46] Creating resource from OpenData
[START] [2020-11-19 12:40:46] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 12:40:46] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 12:40:46] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 12:40:46] Creating resource from OpenData
[START] [2020-11-19 12:40:46] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 12:40:46] create_harvest_instance
[STOP] [2020-11-19 12:40:48] create_harvest_instance
[START] [2020-11-19 12:40:48] fetch_files
[STOP] [2020-11-19 12:40:48] fetch_files
[START] [2020-11-19 12:40:48] validate_each_file
[STOP] [2020-11-19 12:40:48] validate_each_file
[START] [2020-11-19 12:40:48] convert_to_csv
[CMD] [2020-11-19 12:40:48] /usr/bin/sort /app/public/converted_csv/maddison_et_al_m_refs_24390.csv > /app/public/converted_csv/maddison_et_al_m_refs_24390.csv_sorted
[CMD] [2020-11-19 12:40:48] /usr/bin/sort /app/public/converted_csv/maddison_et_al_m_nodes_24391.csv > /app/public/converted_csv/maddison_et_al_m_nodes_24391.csv_sorted
[CMD] [2020-11-19 12:40:48] /usr/bin/sort /app/public/converted_csv/maddison_et_al_m_occurrences_24392.csv > /app/public/converted_csv/maddison_et_al_m_occurrences_24392.csv_sorted
[CMD] [2020-11-19 12:40:48] /usr/bin/sort /app/public/converted_csv/maddison_et_al_m_measurements_24393.csv > /app/public/converted_csv/maddison_et_al_m_measurements_24393.csv_sorted
[STOP] [2020-11-19 12:40:48] convert_to_csv
[START] [2020-11-19 12:40:48] calculate_delta
[CMD] [2020-11-19 12:40:48] echo "0a" > /app/public/diff/maddison_et_al_m_refs_24390.diff
[CMD] [2020-11-19 12:40:48] tail -n +1 /app/public/converted_csv/maddison_et_al_m_refs_24390.csv >> /app/public/diff/maddison_et_al_m_refs_24390.diff
[CMD] [2020-11-19 12:40:48] echo "." >> /app/public/diff/maddison_et_al_m_refs_24390.diff
[CMD] [2020-11-19 12:40:48] echo "0a" > /app/public/diff/maddison_et_al_m_nodes_24391.diff
[CMD] [2020-11-19 12:40:48] tail -n +1 /app/public/converted_csv/maddison_et_al_m_nodes_24391.csv >> /app/public/diff/maddison_et_al_m_nodes_24391.diff
[CMD] [2020-11-19 12:40:48] echo "." >> /app/public/diff/maddison_et_al_m_nodes_24391.diff
[CMD] [2020-11-19 12:40:48] echo "0a" > /app/public/diff/maddison_et_al_m_occurrences_24392.diff
[CMD] [2020-11-19 12:40:48] tail -n +1 /app/public/converted_csv/maddison_et_al_m_occurrences_24392.csv >> /app/public/diff/maddison_et_al_m_occurrences_24392.diff
[CMD] [2020-11-19 12:40:48] echo "." >> /app/public/diff/maddison_et_al_m_occurrences_24392.diff
[CMD] [2020-11-19 12:40:48] echo "0a" > /app/public/diff/maddison_et_al_m_measurements_24393.diff
[CMD] [2020-11-19 12:40:48] tail -n +1 /app/public/converted_csv/maddison_et_al_m_measurements_24393.csv >> /app/public/diff/maddison_et_al_m_measurements_24393.diff
[CMD] [2020-11-19 12:40:48] echo "." >> /app/public/diff/maddison_et_al_m_measurements_24393.diff
[STOP] [2020-11-19 12:40:48] calculate_delta
[START] [2020-11-19 12:40:48] parse_diff_and_store
[INFO] [2020-11-19 12:40:48] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 12:40:48] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 12:40:48] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 12:40:48] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-19 12:40:49] Storing 22 ScientificNames
[INFO] [2020-11-19 12:40:49] Processing group of 22 in 1 groups of 1000
[INFO] [2020-11-19 12:40:49] Average Time: 0.02
[INFO] [2020-11-19 12:40:49] Total Time: 1s
[INFO] [2020-11-19 12:40:49] Storing 22 Nodes
[INFO] [2020-11-19 12:40:49] Processing group of 22 in 1 groups of 1000
[INFO] [2020-11-19 12:40:49] Average Time: 0.03
[INFO] [2020-11-19 12:40:49] Total Time: 1s
[INFO] [2020-11-19 12:40:49] Storing 22 Occurrences
[INFO] [2020-11-19 12:40:49] Processing group of 22 in 1 groups of 1000
[INFO] [2020-11-19 12:40:49] Average Time: 0.03
[INFO] [2020-11-19 12:40:49] Total Time: 1s
[INFO] [2020-11-19 12:40:49] Storing 44 Traits
[INFO] [2020-11-19 12:40:49] Processing group of 44 in 1 groups of 1000
[INFO] [2020-11-19 12:40:50] Average Time: 0.05
[INFO] [2020-11-19 12:40:50] Total Time: 1s
[INFO] [2020-11-19 12:40:50] Storing 22 MetaTraits
[INFO] [2020-11-19 12:40:50] Processing group of 22 in 1 groups of 1000
[INFO] [2020-11-19 12:40:50] Average Time: 0.01
[INFO] [2020-11-19 12:40:50] Total Time: 1s
[STOP] [2020-11-19 12:40:50] parse_diff_and_store
[START] [2020-11-19 12:40:50] resolve_keys
[INFO] [2020-11-19 12:40:55] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-19 12:40:55] traits to occurrences...
[INFO] [2020-11-19 12:40:55] traits to nodes (through occurrences)...
[INFO] [2020-11-19 12:40:55] Traits to sex term...
[INFO] [2020-11-19 12:40:55] Traits to lifestage term...
[INFO] [2020-11-19 12:40:55] MetaTraits to traits...
[INFO] [2020-11-19 12:40:55] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-19 12:40:55] Assocs to occurrences...
[INFO] [2020-11-19 12:40:55] Assocs to nodes...
[INFO] [2020-11-19 12:40:55] Assoc to sex term...
[INFO] [2020-11-19 12:40:55] Assoc to lifestage term...
[INFO] [2020-11-19 12:40:55] MetaAssoc to assocs...
[STOP] [2020-11-19 12:40:55] resolve_keys
[START] [2020-11-19 12:40:55] hold_for_later_1
[STOP] [2020-11-19 12:40:55] hold_for_later_1
[START] [2020-11-19 12:40:55] hold_for_later_2
[STOP] [2020-11-19 12:40:55] hold_for_later_2
[START] [2020-11-19 12:40:55] resolve_missing_parents
[STOP] [2020-11-19 12:40:56] resolve_missing_parents
[START] [2020-11-19 12:40:56] rebuild_nodes
[START] [2020-11-19 12:40:56] Flattener#flatten
[START] [2020-11-19 12:40:56] Flattener#study_resource
[START] [2020-11-19 12:40:56] Flattener#build_ancestry
[STOP] [2020-11-19 12:40:56] Flattener#build_ancestry
[INFO] [2020-11-19 12:40:56] 22 ancestry keys
[START] [2020-11-19 12:40:56] build_node_ancestors
[INFO] [2020-11-19 12:40:56] old ancestors deleted.
[STOP] [2020-11-19 12:40:56] build_node_ancestors
[WARN] [2020-11-19 12:40:56] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-19 12:40:56] Flattener#flatten
[STOP] [2020-11-19 12:40:56] rebuild_nodes
[START] [2020-11-19 12:40:56] resolve_missing_media_owners
[STOP] [2020-11-19 12:40:56] resolve_missing_media_owners
[START] [2020-11-19 12:40:56] sanitize_media_verbatims
[STOP] [2020-11-19 12:40:56] sanitize_media_verbatims
[START] [2020-11-19 12:40:56] queue_downloads
[STOP] [2020-11-19 12:40:56] queue_downloads
[START] [2020-11-19 12:40:56] parse_names
[WARN] [2020-11-19 12:40:56] I see 22 names which still need to be parsed.
[STOP] [2020-11-19 12:40:57] parse_names
[START] [2020-11-19 12:40:57] denormalize_canonical_names_to_nodes
[STOP] [2020-11-19 12:40:57] denormalize_canonical_names_to_nodes
[START] [2020-11-19 12:40:57] match_nodes
[START] [2020-11-19 12:40:57] map_all_nodes_to_pages
[STOP] [2020-11-19 12:40:57] map_all_nodes_to_pages
[INFO] [2020-11-19 12:40:57] ZERO unmatched nodes (of 22)! Nicely done.
[START] [2020-11-19 12:40:57] update_nodes
[STOP] [2020-11-19 12:40:57] update_nodes
[STOP] [2020-11-19 12:40:57] match_nodes
[START] [2020-11-19 12:40:57] reindex_search
[STOP] [2020-11-19 12:40:57] reindex_search
[START] [2020-11-19 12:40:57] normalize_units
[STOP] [2020-11-19 12:40:57] normalize_units
[START] [2020-11-19 12:40:57] calculate_statistics
[2020-11-19 12:40:57] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-19 12:40:57] calculate_statistics
[START] [2020-11-19 12:40:57] complete_harvest_instance
[START] [2020-11-19 12:40:57] overall_tsv_creation
[INFO] [2020-11-19 12:40:57] Processing group of 22 in 1 batches of 10000
[INFO] [2020-11-19 12:41:40] 22 Traits (unfiltered)...
[INFO] [2020-11-19 12:42:25] 22 Traits (filtered)...
[INFO] [2020-11-19 12:42:25] 0 Associations (filtered)...
[INFO] [2020-11-19 12:42:25] 44 metadata added.
[INFO] [2020-11-19 12:42:25] 0 metadata added.
[INFO] [2020-11-19 12:42:25] Average Time: 68.68
[INFO] [2020-11-19 12:42:25] Total Time: 1m29s
[STOP] [2020-11-19 12:42:25] overall_tsv_creation
[INFO] [2020-11-19 12:42:25] Done. Check your files:
[INFO] [2020-11-19 12:42:25] (22 lines) /app/public/data/maddison_et_al_m/publish_nodes.tsv
[INFO] [2020-11-19 12:42:25] (22 lines) /app/public/data/maddison_et_al_m/publish_scientific_names.tsv
[INFO] [2020-11-19 12:42:25] (23 lines) /app/public/data/maddison_et_al_m/publish_traits.tsv
[INFO] [2020-11-19 12:42:25] (45 lines) /app/public/data/maddison_et_al_m/publish_metadata.tsv
[STOP] [2020-11-19 12:42:25] complete_harvest_instance
[START] [2020-11-19 12:42:25] completed
[STOP] [2020-11-19 12:42:25] completed
[STOP] [2020-11-19 12:42:25] logged process, took 98.85
[INFO] [2021-04-19 09:41:12] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 09:41:15] ## remove_type: ScientificName
[INFO] [2021-04-19 09:41:15] ++ Calling delete_all on 22 instances...
[INFO] [2021-04-19 09:41:15] [09:41:15.394] Removed 22 Scientificnames
[INFO] [2021-04-19 09:41:15] ## remove_type: Vernacular
[INFO] [2021-04-19 09:41:15] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:41:15] [09:41:15.396] Removed 0 Vernaculars
[INFO] [2021-04-19 09:41:15] ## remove_type: Article
[INFO] [2021-04-19 09:41:15] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:41:15] [09:41:15.397] Removed 0 Articles
[INFO] [2021-04-19 09:41:15] ## remove_type: Medium
[INFO] [2021-04-19 09:41:15] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:41:15] [09:41:15.399] Removed 0 Media
[INFO] [2021-04-19 09:41:15] ## remove_type: Trait
[INFO] [2021-04-19 09:41:15] ++ Calling delete_all on 44 instances...
[INFO] [2021-04-19 09:41:15] [09:41:15.401] Removed 44 Traits
[INFO] [2021-04-19 09:41:15] ## remove_type: MetaTrait
[INFO] [2021-04-19 09:41:15] ++ Calling delete_all on 22 instances...
[INFO] [2021-04-19 09:41:15] [09:41:15.403] Removed 22 Metatraits
[INFO] [2021-04-19 09:41:15] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 09:41:15] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:41:15] [09:41:15.405] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 09:41:15] ## remove_type: Assoc
[INFO] [2021-04-19 09:41:15] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:41:15] [09:41:15.406] Removed 0 Assocs
[INFO] [2021-04-19 09:41:15] ## remove_type: MetaAssoc
[INFO] [2021-04-19 09:41:15] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:41:15] [09:41:15.408] Removed 0 Metaassocs
[INFO] [2021-04-19 09:41:15] ## remove_type: Identifier
[INFO] [2021-04-19 09:41:15] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:41:15] [09:41:15.409] Removed 0 Identifiers
[INFO] [2021-04-19 09:41:15] ## remove_type: Reference
[INFO] [2021-04-19 09:41:15] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:41:15] [09:41:15.411] Removed 0 References
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:15] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] Starting batch with ID 84620756...
[INFO] [2021-04-19 09:41:16] ## remove_type: Node
[INFO] [2021-04-19 09:41:16] ++ Calling delete_all on 22 instances...
[INFO] [2021-04-19 09:41:16] [09:41:16.329] Removed 22 Nodes
[START] [2021-04-19 09:41:16] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 09:41:16] Creating resource from OpenData
[START] [2021-04-19 09:41:17] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 09:41:17] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 09:41:22] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 09:41:22] Creating resource from OpenData
[START] [2021-04-19 09:41:23] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 09:41:23] create_harvest_instance
[INFO] [2021-04-19 09:41:23] Created harvest instance #3719
[STOP] [2021-04-19 09:41:23] create_harvest_instance
[START] [2021-04-19 09:41:23] fetch_files
[STOP] [2021-04-19 09:41:23] fetch_files
[START] [2021-04-19 09:41:23] validate_each_file
[INFO] [2021-04-19 09:41:23] Looping over 4 formats...
[INFO] [2021-04-19 09:41:23] ...refs (/app/public/data/maddison_et_al_m/references.tsv)
[INFO] [2021-04-19 09:41:23] Valid: /app/public/converted_csv/maddison_et_al_m_refs_3719.csv (0 lines)
[INFO] [2021-04-19 09:41:23] ...nodes (/app/public/data/maddison_et_al_m/taxa.txt)
[INFO] [2021-04-19 09:41:23] Valid: /app/public/converted_csv/maddison_et_al_m_nodes_3719.csv (22 lines)
[INFO] [2021-04-19 09:41:23] ...occurrences (/app/public/data/maddison_et_al_m/occurrences.txt)
[INFO] [2021-04-19 09:41:23] Valid: /app/public/converted_csv/maddison_et_al_m_occurrences_3719.csv (22 lines)
[INFO] [2021-04-19 09:41:23] ...measurements (/app/public/data/maddison_et_al_m/measurementsorfacts.txt)
[INFO] [2021-04-19 09:41:23] Valid: /app/public/converted_csv/maddison_et_al_m_measurements_3719.csv (44 lines)
[STOP] [2021-04-19 09:41:23] validate_each_file
[START] [2021-04-19 09:41:23] convert_to_csv
[INFO] [2021-04-19 09:41:23] Looping over 4 formats...
[INFO] [2021-04-19 09:41:23] ...refs (/app/public/data/maddison_et_al_m/references.tsv)
[CMD] [2021-04-19 09:41:23] /usr/bin/sort /app/public/converted_csv/maddison_et_al_m_refs_3719.csv > /app/public/converted_csv/maddison_et_al_m_refs_3719.csv_sorted
[INFO] [2021-04-19 09:41:23] Converted: /app/public/converted_csv/maddison_et_al_m_refs_3719.csv (0 lines)
[INFO] [2021-04-19 09:41:23] ...nodes (/app/public/data/maddison_et_al_m/taxa.txt)
[CMD] [2021-04-19 09:41:23] /usr/bin/sort /app/public/converted_csv/maddison_et_al_m_nodes_3719.csv > /app/public/converted_csv/maddison_et_al_m_nodes_3719.csv_sorted
[INFO] [2021-04-19 09:41:24] Converted: /app/public/converted_csv/maddison_et_al_m_nodes_3719.csv (22 lines)
[INFO] [2021-04-19 09:41:24] ...occurrences (/app/public/data/maddison_et_al_m/occurrences.txt)
[CMD] [2021-04-19 09:41:24] /usr/bin/sort /app/public/converted_csv/maddison_et_al_m_occurrences_3719.csv > /app/public/converted_csv/maddison_et_al_m_occurrences_3719.csv_sorted
[INFO] [2021-04-19 09:41:24] Converted: /app/public/converted_csv/maddison_et_al_m_occurrences_3719.csv (22 lines)
[INFO] [2021-04-19 09:41:24] ...measurements (/app/public/data/maddison_et_al_m/measurementsorfacts.txt)
[CMD] [2021-04-19 09:41:24] /usr/bin/sort /app/public/converted_csv/maddison_et_al_m_measurements_3719.csv > /app/public/converted_csv/maddison_et_al_m_measurements_3719.csv_sorted
[INFO] [2021-04-19 09:41:24] Converted: /app/public/converted_csv/maddison_et_al_m_measurements_3719.csv (44 lines)
[STOP] [2021-04-19 09:41:24] convert_to_csv
[START] [2021-04-19 09:41:24] calculate_delta
[INFO] [2021-04-19 09:41:24] Looping over 4 formats...
[INFO] [2021-04-19 09:41:24] ...refs (/app/public/data/maddison_et_al_m/references.tsv)
[CMD] [2021-04-19 09:41:24] echo "0a" > /app/public/diff/maddison_et_al_m_refs_3719.diff
[CMD] [2021-04-19 09:41:25] tail -n +1 /app/public/converted_csv/maddison_et_al_m_refs_3719.csv >> /app/public/diff/maddison_et_al_m_refs_3719.diff
[CMD] [2021-04-19 09:41:25] echo "." >> /app/public/diff/maddison_et_al_m_refs_3719.diff
[INFO] [2021-04-19 09:41:25] Created diff: /app/public/diff/maddison_et_al_m_refs_3719.diff (2 lines)
[INFO] [2021-04-19 09:41:25] ...nodes (/app/public/data/maddison_et_al_m/taxa.txt)
[CMD] [2021-04-19 09:41:25] echo "0a" > /app/public/diff/maddison_et_al_m_nodes_3719.diff
[CMD] [2021-04-19 09:41:26] tail -n +1 /app/public/converted_csv/maddison_et_al_m_nodes_3719.csv >> /app/public/diff/maddison_et_al_m_nodes_3719.diff
[CMD] [2021-04-19 09:41:26] echo "." >> /app/public/diff/maddison_et_al_m_nodes_3719.diff
[INFO] [2021-04-19 09:41:27] Created diff: /app/public/diff/maddison_et_al_m_nodes_3719.diff (24 lines)
[INFO] [2021-04-19 09:41:27] ...occurrences (/app/public/data/maddison_et_al_m/occurrences.txt)
[CMD] [2021-04-19 09:41:27] echo "0a" > /app/public/diff/maddison_et_al_m_occurrences_3719.diff
[CMD] [2021-04-19 09:41:27] tail -n +1 /app/public/converted_csv/maddison_et_al_m_occurrences_3719.csv >> /app/public/diff/maddison_et_al_m_occurrences_3719.diff
[CMD] [2021-04-19 09:41:27] echo "." >> /app/public/diff/maddison_et_al_m_occurrences_3719.diff
[INFO] [2021-04-19 09:41:28] Created diff: /app/public/diff/maddison_et_al_m_occurrences_3719.diff (24 lines)
[INFO] [2021-04-19 09:41:28] ...measurements (/app/public/data/maddison_et_al_m/measurementsorfacts.txt)
[CMD] [2021-04-19 09:41:28] echo "0a" > /app/public/diff/maddison_et_al_m_measurements_3719.diff
[CMD] [2021-04-19 09:41:28] tail -n +1 /app/public/converted_csv/maddison_et_al_m_measurements_3719.csv >> /app/public/diff/maddison_et_al_m_measurements_3719.diff
[CMD] [2021-04-19 09:41:28] echo "." >> /app/public/diff/maddison_et_al_m_measurements_3719.diff
[INFO] [2021-04-19 09:41:29] Created diff: /app/public/diff/maddison_et_al_m_measurements_3719.diff (46 lines)
[STOP] [2021-04-19 09:41:29] calculate_delta
[START] [2021-04-19 09:41:29] parse_diff_and_store
[INFO] [2021-04-19 09:41:29] Handling diff: /app/public/diff/maddison_et_al_m_refs_3719.diff (2 lines)
[INFO] [2021-04-19 09:41:29] Loading refs diff file into memory (2 /app/public/diff/maddison_et_al_m_refs_3719.diff lines)...
[INFO] [2021-04-19 09:41:30] Handling diff: /app/public/diff/maddison_et_al_m_nodes_3719.diff (24 lines)
[INFO] [2021-04-19 09:41:30] Loading nodes diff file into memory (24 /app/public/diff/maddison_et_al_m_nodes_3719.diff lines)...
[INFO] [2021-04-19 09:41:31] Handling diff: /app/public/diff/maddison_et_al_m_occurrences_3719.diff (24 lines)
[INFO] [2021-04-19 09:41:31] Loading occurrences diff file into memory (24 /app/public/diff/maddison_et_al_m_occurrences_3719.diff lines)...
[INFO] [2021-04-19 09:41:31] Handling diff: /app/public/diff/maddison_et_al_m_measurements_3719.diff (46 lines)
[INFO] [2021-04-19 09:41:32] Loading measurements diff file into memory (46 /app/public/diff/maddison_et_al_m_measurements_3719.diff lines)...
[INFO] [2021-04-19 09:41:32] Storing 22 ScientificNames
[INFO] [2021-04-19 09:41:32] Processing group of 22 in 1 groups of 1000
[INFO] [2021-04-19 09:41:32] Average Time: 0.01
[INFO] [2021-04-19 09:41:32] Total Time: 1s
[INFO] [2021-04-19 09:41:32] Storing 22 Nodes
[INFO] [2021-04-19 09:41:32] Processing group of 22 in 1 groups of 1000
[INFO] [2021-04-19 09:41:32] Average Time: 0.01
[INFO] [2021-04-19 09:41:32] Total Time: 1s
[INFO] [2021-04-19 09:41:32] Storing 22 Occurrences
[INFO] [2021-04-19 09:41:32] Processing group of 22 in 1 groups of 1000
[INFO] [2021-04-19 09:41:32] Average Time: 0.0
[INFO] [2021-04-19 09:41:32] Total Time: 1s
[INFO] [2021-04-19 09:41:32] Storing 44 Traits
[INFO] [2021-04-19 09:41:32] Processing group of 44 in 1 groups of 1000
[INFO] [2021-04-19 09:41:32] Average Time: 0.01
[INFO] [2021-04-19 09:41:32] Total Time: 1s
[INFO] [2021-04-19 09:41:32] Storing 22 MetaTraits
[INFO] [2021-04-19 09:41:32] Processing group of 22 in 1 groups of 1000
[INFO] [2021-04-19 09:41:32] Average Time: 0.0
[INFO] [2021-04-19 09:41:32] Total Time: 1s
[STOP] [2021-04-19 09:41:32] parse_diff_and_store
[START] [2021-04-19 09:41:32] resolve_keys
[INFO] [2021-04-19 09:41:38] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 09:41:38] traits to occurrences...
[INFO] [2021-04-19 09:41:38] traits to nodes (through occurrences)...
[INFO] [2021-04-19 09:41:38] Traits to sex term...
[INFO] [2021-04-19 09:41:38] Traits to lifestage term...
[INFO] [2021-04-19 09:41:38] MetaTraits to traits...
[INFO] [2021-04-19 09:41:38] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 09:41:38] Assocs to occurrences...
[INFO] [2021-04-19 09:41:38] Assocs to nodes...
[INFO] [2021-04-19 09:41:38] Assoc to sex term...
[INFO] [2021-04-19 09:41:38] Assoc to lifestage term...
[INFO] [2021-04-19 09:41:38] MetaAssoc to assocs...
[STOP] [2021-04-19 09:41:38] resolve_keys
[START] [2021-04-19 09:41:38] hold_for_later_1
[STOP] [2021-04-19 09:41:38] hold_for_later_1
[START] [2021-04-19 09:41:38] hold_for_later_2
[STOP] [2021-04-19 09:41:38] hold_for_later_2
[START] [2021-04-19 09:41:38] resolve_missing_parents
[STOP] [2021-04-19 09:41:38] resolve_missing_parents
[START] [2021-04-19 09:41:38] rebuild_nodes
[START] [2021-04-19 09:41:38] Flattener#flatten
[START] [2021-04-19 09:41:38] Flattener#study_resource
[START] [2021-04-19 09:41:38] Flattener#build_ancestry
[STOP] [2021-04-19 09:41:38] Flattener#build_ancestry
[INFO] [2021-04-19 09:41:38] 22 ancestry keys
[START] [2021-04-19 09:41:38] build_node_ancestors
[INFO] [2021-04-19 09:41:38] old ancestors deleted.
[STOP] [2021-04-19 09:41:38] build_node_ancestors
[WARN] [2021-04-19 09:41:38] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 09:41:38] Flattener#flatten
[STOP] [2021-04-19 09:41:38] rebuild_nodes
[START] [2021-04-19 09:41:38] resolve_missing_media_owners
[STOP] [2021-04-19 09:41:38] resolve_missing_media_owners
[START] [2021-04-19 09:41:38] sanitize_media_verbatims
[STOP] [2021-04-19 09:41:38] sanitize_media_verbatims
[START] [2021-04-19 09:41:38] queue_downloads
[STOP] [2021-04-19 09:41:38] queue_downloads
[START] [2021-04-19 09:41:38] parse_names
[WARN] [2021-04-19 09:41:38] I see 22 names which still need to be parsed.
[STOP] [2021-04-19 09:41:39] parse_names
[START] [2021-04-19 09:41:39] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 09:41:39] denormalize_canonical_names_to_nodes
[START] [2021-04-19 09:41:39] match_nodes
[START] [2021-04-19 09:41:39] map_all_nodes_to_pages
[STOP] [2021-04-19 09:41:39] map_all_nodes_to_pages
[INFO] [2021-04-19 09:41:39] ZERO unmatched nodes (of 22)! Nicely done.
[START] [2021-04-19 09:41:39] update_nodes
[STOP] [2021-04-19 09:41:39] update_nodes
[STOP] [2021-04-19 09:41:39] match_nodes
[START] [2021-04-19 09:41:39] reindex_search
[STOP] [2021-04-19 09:41:39] reindex_search
[START] [2021-04-19 09:41:39] normalize_units
[STOP] [2021-04-19 09:41:39] normalize_units
[START] [2021-04-19 09:41:39] calculate_statistics
[2021-04-19 09:41:39] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 09:41:39] calculate_statistics
[START] [2021-04-19 09:41:39] complete_harvest_instance
[START] [2021-04-19 09:41:39] overall_tsv_creation
[INFO] [2021-04-19 09:41:39] Processing group of 22 in 1 batches of 10000
[INFO] [2021-04-19 09:42:16] 22 Traits (unfiltered)...
[INFO] [2021-04-19 09:42:50] 22 Traits (filtered)...
[INFO] [2021-04-19 09:42:50] 0 Associations (filtered)...
[INFO] [2021-04-19 09:42:50] 22 metadata added.
[INFO] [2021-04-19 09:42:50] 0 metadata added.
[INFO] [2021-04-19 09:43:16] Average Time: 72.07
[INFO] [2021-04-19 09:43:16] Total Time: 1m37s
[STOP] [2021-04-19 09:43:16] overall_tsv_creation
[INFO] [2021-04-19 09:43:16] Done. Check your files:
[INFO] [2021-04-19 09:43:16] (22 lines) /app/public/data/maddison_et_al_m/publish_nodes.tsv
[INFO] [2021-04-19 09:43:17] (22 lines) /app/public/data/maddison_et_al_m/publish_scientific_names.tsv
[INFO] [2021-04-19 09:43:17] (23 lines) /app/public/data/maddison_et_al_m/publish_traits.tsv
[INFO] [2021-04-19 09:43:17] (23 lines) /app/public/data/maddison_et_al_m/publish_metadata.tsv
[STOP] [2021-04-19 09:43:18] complete_harvest_instance
[START] [2021-04-19 09:43:18] completed
[STOP] [2021-04-19 09:43:18] completed
[STOP] [2021-04-19 09:43:18] logged process, took 115.35

Latest Process

19 Apr 09:41 EXITED currently processing 0