Harvest for Syme and Oakley 2012 Created 19 Apr 09:48

Harvesting Log

# Logfile created on 2020-08-27 15:35:55 -0400 by logger.rb/v1.4.2
[START] [2020-08-27 15:35:55] logged process
[START] [2020-08-27 15:35:55] Creating resource from OpenData
[START] [2020-08-27 15:35:56] logged process
[START] [2020-08-27 15:35:56] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:35:56] Parse meta.xml file and create formats with fields
[STOP] [2020-08-27 15:35:56] Creating resource from OpenData
[INFO] [2020-11-19 13:56:00] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-11-19 13:56:03] ## remove_type: ScientificName
[INFO] [2020-11-19 13:56:03] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:56:03] [13:56:03.704] Removed 0 Scientificnames
[INFO] [2020-11-19 13:56:03] ## remove_type: Vernacular
[INFO] [2020-11-19 13:56:03] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:56:03] [13:56:03.707] Removed 0 Vernaculars
[INFO] [2020-11-19 13:56:03] ## remove_type: Article
[INFO] [2020-11-19 13:56:03] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:56:03] [13:56:03.710] Removed 0 Articles
[INFO] [2020-11-19 13:56:03] ## remove_type: Medium
[INFO] [2020-11-19 13:56:03] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:56:03] [13:56:03.714] Removed 0 Media
[INFO] [2020-11-19 13:56:03] ## remove_type: Trait
[INFO] [2020-11-19 13:56:03] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:56:03] [13:56:03.717] Removed 0 Traits
[INFO] [2020-11-19 13:56:03] ## remove_type: MetaTrait
[INFO] [2020-11-19 13:56:03] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:56:03] [13:56:03.719] Removed 0 Metatraits
[INFO] [2020-11-19 13:56:03] ## remove_type: OccurrenceMetadatum
[INFO] [2020-11-19 13:56:03] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:56:03] [13:56:03.722] Removed 0 Occurrencemetadata
[INFO] [2020-11-19 13:56:03] ## remove_type: Assoc
[INFO] [2020-11-19 13:56:03] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:56:03] [13:56:03.725] Removed 0 Assocs
[INFO] [2020-11-19 13:56:03] ## remove_type: MetaAssoc
[INFO] [2020-11-19 13:56:03] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:56:03] [13:56:03.728] Removed 0 Metaassocs
[INFO] [2020-11-19 13:56:03] ## remove_type: Identifier
[INFO] [2020-11-19 13:56:03] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:56:03] [13:56:03.730] Removed 0 Identifiers
[INFO] [2020-11-19 13:56:03] ## remove_type: Reference
[INFO] [2020-11-19 13:56:03] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:56:03] [13:56:03.733] Removed 0 References
[INFO] [2020-11-19 13:56:03] ## remove_type: Node
[INFO] [2020-11-19 13:56:03] ++ Calling delete_all on 0 instances...
[INFO] [2020-11-19 13:56:03] [13:56:03.767] Removed 0 Nodes
[START] [2020-11-19 13:56:03] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:56:03] Creating resource from OpenData
[START] [2020-11-19 13:56:04] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:56:04] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:56:04] Parse meta.xml file and create formats with fields
[STOP] [2020-11-19 13:56:04] Creating resource from OpenData
[START] [2020-11-19 13:56:04] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979

[START] [2020-11-19 13:56:04] create_harvest_instance
[STOP] [2020-11-19 13:56:05] create_harvest_instance
[START] [2020-11-19 13:56:05] fetch_files
[STOP] [2020-11-19 13:56:05] fetch_files
[START] [2020-11-19 13:56:05] validate_each_file
[STOP] [2020-11-19 13:56:05] validate_each_file
[START] [2020-11-19 13:56:05] convert_to_csv
[CMD] [2020-11-19 13:56:05] /usr/bin/sort /app/public/converted_csv/syme_oakley_syme_refs_24486.csv > /app/public/converted_csv/syme_oakley_syme_refs_24486.csv_sorted
[CMD] [2020-11-19 13:56:05] /usr/bin/sort /app/public/converted_csv/syme_oakley_syme_nodes_24487.csv > /app/public/converted_csv/syme_oakley_syme_nodes_24487.csv_sorted
[CMD] [2020-11-19 13:56:05] /usr/bin/sort /app/public/converted_csv/syme_oakley_syme_occurrences_24488.csv > /app/public/converted_csv/syme_oakley_syme_occurrences_24488.csv_sorted
[CMD] [2020-11-19 13:56:05] /usr/bin/sort /app/public/converted_csv/syme_oakley_syme_measurements_24489.csv > /app/public/converted_csv/syme_oakley_syme_measurements_24489.csv_sorted
[STOP] [2020-11-19 13:56:05] convert_to_csv
[START] [2020-11-19 13:56:05] calculate_delta
[CMD] [2020-11-19 13:56:05] echo "0a" > /app/public/diff/syme_oakley_syme_refs_24486.diff
[CMD] [2020-11-19 13:56:05] tail -n +1 /app/public/converted_csv/syme_oakley_syme_refs_24486.csv >> /app/public/diff/syme_oakley_syme_refs_24486.diff
[CMD] [2020-11-19 13:56:05] echo "." >> /app/public/diff/syme_oakley_syme_refs_24486.diff
[CMD] [2020-11-19 13:56:05] echo "0a" > /app/public/diff/syme_oakley_syme_nodes_24487.diff
[CMD] [2020-11-19 13:56:05] tail -n +1 /app/public/converted_csv/syme_oakley_syme_nodes_24487.csv >> /app/public/diff/syme_oakley_syme_nodes_24487.diff
[CMD] [2020-11-19 13:56:05] echo "." >> /app/public/diff/syme_oakley_syme_nodes_24487.diff
[CMD] [2020-11-19 13:56:05] echo "0a" > /app/public/diff/syme_oakley_syme_occurrences_24488.diff
[CMD] [2020-11-19 13:56:06] tail -n +1 /app/public/converted_csv/syme_oakley_syme_occurrences_24488.csv >> /app/public/diff/syme_oakley_syme_occurrences_24488.diff
[CMD] [2020-11-19 13:56:06] echo "." >> /app/public/diff/syme_oakley_syme_occurrences_24488.diff
[CMD] [2020-11-19 13:56:06] echo "0a" > /app/public/diff/syme_oakley_syme_measurements_24489.diff
[CMD] [2020-11-19 13:56:06] tail -n +1 /app/public/converted_csv/syme_oakley_syme_measurements_24489.csv >> /app/public/diff/syme_oakley_syme_measurements_24489.diff
[CMD] [2020-11-19 13:56:06] echo "." >> /app/public/diff/syme_oakley_syme_measurements_24489.diff
[STOP] [2020-11-19 13:56:06] calculate_delta
[START] [2020-11-19 13:56:06] parse_diff_and_store
[INFO] [2020-11-19 13:56:06] Loading refs diff file into memory (true lines)...
[INFO] [2020-11-19 13:56:06] Loading nodes diff file into memory (true lines)...
[INFO] [2020-11-19 13:56:06] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-11-19 13:56:06] Loading measurements diff file into memory (true lines)...
[INFO] [2020-11-19 13:56:07] Storing 101 ScientificNames
[INFO] [2020-11-19 13:56:07] Processing group of 101 in 1 groups of 1000
[INFO] [2020-11-19 13:56:07] Average Time: 0.05
[INFO] [2020-11-19 13:56:07] Total Time: 1s
[INFO] [2020-11-19 13:56:07] Storing 101 Nodes
[INFO] [2020-11-19 13:56:07] Processing group of 101 in 1 groups of 1000
[INFO] [2020-11-19 13:56:07] Average Time: 0.07
[INFO] [2020-11-19 13:56:07] Total Time: 1s
[INFO] [2020-11-19 13:56:07] Storing 101 Occurrences
[INFO] [2020-11-19 13:56:07] Processing group of 101 in 1 groups of 1000
[INFO] [2020-11-19 13:56:07] Average Time: 0.07
[INFO] [2020-11-19 13:56:07] Total Time: 1s
[INFO] [2020-11-19 13:56:07] Storing 106 Traits
[INFO] [2020-11-19 13:56:07] Processing group of 106 in 1 groups of 1000
[INFO] [2020-11-19 13:56:07] Average Time: 0.1
[INFO] [2020-11-19 13:56:07] Total Time: 1s
[INFO] [2020-11-19 13:56:07] Storing 101 MetaTraits
[INFO] [2020-11-19 13:56:07] Processing group of 101 in 1 groups of 1000
[INFO] [2020-11-19 13:56:07] Average Time: 0.02
[INFO] [2020-11-19 13:56:07] Total Time: 1s
[STOP] [2020-11-19 13:56:07] parse_diff_and_store
[START] [2020-11-19 13:56:07] resolve_keys
[INFO] [2020-11-19 13:56:13] Occurrences to nodes (through scientific_names)...
[INFO] [2020-11-19 13:56:13] traits to occurrences...
[INFO] [2020-11-19 13:56:13] traits to nodes (through occurrences)...
[INFO] [2020-11-19 13:56:13] Traits to sex term...
[INFO] [2020-11-19 13:56:13] Traits to lifestage term...
[INFO] [2020-11-19 13:56:13] MetaTraits to traits...
[INFO] [2020-11-19 13:56:13] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-11-19 13:56:13] Assocs to occurrences...
[INFO] [2020-11-19 13:56:13] Assocs to nodes...
[INFO] [2020-11-19 13:56:13] Assoc to sex term...
[INFO] [2020-11-19 13:56:13] Assoc to lifestage term...
[INFO] [2020-11-19 13:56:13] MetaAssoc to assocs...
[STOP] [2020-11-19 13:56:13] resolve_keys
[START] [2020-11-19 13:56:13] hold_for_later_1
[STOP] [2020-11-19 13:56:13] hold_for_later_1
[START] [2020-11-19 13:56:13] hold_for_later_2
[STOP] [2020-11-19 13:56:13] hold_for_later_2
[START] [2020-11-19 13:56:13] resolve_missing_parents
[STOP] [2020-11-19 13:56:13] resolve_missing_parents
[START] [2020-11-19 13:56:13] rebuild_nodes
[START] [2020-11-19 13:56:13] Flattener#flatten
[START] [2020-11-19 13:56:13] Flattener#study_resource
[START] [2020-11-19 13:56:13] Flattener#build_ancestry
[STOP] [2020-11-19 13:56:13] Flattener#build_ancestry
[INFO] [2020-11-19 13:56:13] 101 ancestry keys
[START] [2020-11-19 13:56:13] build_node_ancestors
[INFO] [2020-11-19 13:56:13] old ancestors deleted.
[STOP] [2020-11-19 13:56:13] build_node_ancestors
[WARN] [2020-11-19 13:56:13] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-11-19 13:56:13] Flattener#flatten
[STOP] [2020-11-19 13:56:13] rebuild_nodes
[START] [2020-11-19 13:56:13] resolve_missing_media_owners
[STOP] [2020-11-19 13:56:13] resolve_missing_media_owners
[START] [2020-11-19 13:56:13] sanitize_media_verbatims
[STOP] [2020-11-19 13:56:13] sanitize_media_verbatims
[START] [2020-11-19 13:56:13] queue_downloads
[STOP] [2020-11-19 13:56:13] queue_downloads
[START] [2020-11-19 13:56:13] parse_names
[WARN] [2020-11-19 13:56:13] I see 101 names which still need to be parsed.
[STOP] [2020-11-19 13:56:15] parse_names
[START] [2020-11-19 13:56:15] denormalize_canonical_names_to_nodes
[STOP] [2020-11-19 13:56:15] denormalize_canonical_names_to_nodes
[START] [2020-11-19 13:56:15] match_nodes
[START] [2020-11-19 13:56:15] map_all_nodes_to_pages
[STOP] [2020-11-19 13:56:15] map_all_nodes_to_pages
[INFO] [2020-11-19 13:56:15] ZERO unmatched nodes (of 101)! Nicely done.
[START] [2020-11-19 13:56:15] update_nodes
[STOP] [2020-11-19 13:56:15] update_nodes
[STOP] [2020-11-19 13:56:15] match_nodes
[START] [2020-11-19 13:56:15] reindex_search
[STOP] [2020-11-19 13:56:15] reindex_search
[START] [2020-11-19 13:56:15] normalize_units
[STOP] [2020-11-19 13:56:15] normalize_units
[START] [2020-11-19 13:56:15] calculate_statistics
[2020-11-19 13:56:15] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-11-19 13:56:15] calculate_statistics
[START] [2020-11-19 13:56:15] complete_harvest_instance
[START] [2020-11-19 13:56:15] overall_tsv_creation
[INFO] [2020-11-19 13:56:15] Processing group of 101 in 1 batches of 10000
[INFO] [2020-11-19 13:56:59] 101 Traits (unfiltered)...
[INFO] [2020-11-19 13:57:43] 101 Traits (filtered)...
[INFO] [2020-11-19 13:57:43] 0 Associations (filtered)...
[INFO] [2020-11-19 13:57:43] 106 metadata added.
[INFO] [2020-11-19 13:57:43] 0 metadata added.
[INFO] [2020-11-19 13:57:43] Average Time: 68.75
[INFO] [2020-11-19 13:57:43] Total Time: 1m29s
[STOP] [2020-11-19 13:57:43] overall_tsv_creation
[INFO] [2020-11-19 13:57:43] Done. Check your files:
[INFO] [2020-11-19 13:57:43] (101 lines) /app/public/data/syme_oakley_syme/publish_nodes.tsv
[INFO] [2020-11-19 13:57:43] (101 lines) /app/public/data/syme_oakley_syme/publish_scientific_names.tsv
[INFO] [2020-11-19 13:57:43] (102 lines) /app/public/data/syme_oakley_syme/publish_traits.tsv
[INFO] [2020-11-19 13:57:43] (107 lines) /app/public/data/syme_oakley_syme/publish_metadata.tsv
[STOP] [2020-11-19 13:57:44] complete_harvest_instance
[START] [2020-11-19 13:57:44] completed
[STOP] [2020-11-19 13:57:44] completed
[STOP] [2020-11-19 13:57:44] logged process, took 99.75
[INFO] [2021-04-19 09:48:35] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 09:48:38] ## remove_type: ScientificName
[INFO] [2021-04-19 09:48:38] ++ Calling delete_all on 101 instances...
[INFO] [2021-04-19 09:48:38] [09:48:38.609] Removed 101 Scientificnames
[INFO] [2021-04-19 09:48:38] ## remove_type: Vernacular
[INFO] [2021-04-19 09:48:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:48:38] [09:48:38.610] Removed 0 Vernaculars
[INFO] [2021-04-19 09:48:38] ## remove_type: Article
[INFO] [2021-04-19 09:48:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:48:38] [09:48:38.612] Removed 0 Articles
[INFO] [2021-04-19 09:48:38] ## remove_type: Medium
[INFO] [2021-04-19 09:48:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:48:38] [09:48:38.613] Removed 0 Media
[INFO] [2021-04-19 09:48:38] ## remove_type: Trait
[INFO] [2021-04-19 09:48:38] ++ Calling delete_all on 106 instances...
[INFO] [2021-04-19 09:48:38] [09:48:38.617] Removed 106 Traits
[INFO] [2021-04-19 09:48:38] ## remove_type: MetaTrait
[INFO] [2021-04-19 09:48:38] ++ Calling delete_all on 101 instances...
[INFO] [2021-04-19 09:48:38] [09:48:38.620] Removed 101 Metatraits
[INFO] [2021-04-19 09:48:38] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 09:48:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:48:38] [09:48:38.622] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 09:48:38] ## remove_type: Assoc
[INFO] [2021-04-19 09:48:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:48:38] [09:48:38.624] Removed 0 Assocs
[INFO] [2021-04-19 09:48:38] ## remove_type: MetaAssoc
[INFO] [2021-04-19 09:48:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:48:38] [09:48:38.625] Removed 0 Metaassocs
[INFO] [2021-04-19 09:48:38] ## remove_type: Identifier
[INFO] [2021-04-19 09:48:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:48:38] [09:48:38.627] Removed 0 Identifiers
[INFO] [2021-04-19 09:48:38] ## remove_type: Reference
[INFO] [2021-04-19 09:48:38] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 09:48:38] [09:48:38.628] Removed 0 References
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:38] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] Starting batch with ID 84620798...
[INFO] [2021-04-19 09:48:39] ## remove_type: Node
[INFO] [2021-04-19 09:48:39] ++ Calling delete_all on 101 instances...
[INFO] [2021-04-19 09:48:39] [09:48:39.638] Removed 101 Nodes
[START] [2021-04-19 09:48:40] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 09:48:40] Creating resource from OpenData
[START] [2021-04-19 09:48:41] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 09:48:41] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 09:48:45] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 09:48:45] Creating resource from OpenData
[START] [2021-04-19 09:48:46] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 09:48:46] create_harvest_instance
[INFO] [2021-04-19 09:48:46] Created harvest instance #3720
[STOP] [2021-04-19 09:48:46] create_harvest_instance
[START] [2021-04-19 09:48:46] fetch_files
[STOP] [2021-04-19 09:48:46] fetch_files
[START] [2021-04-19 09:48:46] validate_each_file
[INFO] [2021-04-19 09:48:46] Looping over 4 formats...
[INFO] [2021-04-19 09:48:46] ...refs (/app/public/data/syme_oakley_syme/references.tsv)
[INFO] [2021-04-19 09:48:46] Valid: /app/public/converted_csv/syme_oakley_syme_refs_3720.csv (0 lines)
[INFO] [2021-04-19 09:48:46] ...nodes (/app/public/data/syme_oakley_syme/taxa.txt)
[INFO] [2021-04-19 09:48:46] Valid: /app/public/converted_csv/syme_oakley_syme_nodes_3720.csv (101 lines)
[INFO] [2021-04-19 09:48:46] ...occurrences (/app/public/data/syme_oakley_syme/occurrences.txt)
[INFO] [2021-04-19 09:48:46] Valid: /app/public/converted_csv/syme_oakley_syme_occurrences_3720.csv (101 lines)
[INFO] [2021-04-19 09:48:46] ...measurements (/app/public/data/syme_oakley_syme/measurementsorfacts.txt)
[INFO] [2021-04-19 09:48:46] Valid: /app/public/converted_csv/syme_oakley_syme_measurements_3720.csv (106 lines)
[STOP] [2021-04-19 09:48:46] validate_each_file
[START] [2021-04-19 09:48:46] convert_to_csv
[INFO] [2021-04-19 09:48:46] Looping over 4 formats...
[INFO] [2021-04-19 09:48:46] ...refs (/app/public/data/syme_oakley_syme/references.tsv)
[CMD] [2021-04-19 09:48:46] /usr/bin/sort /app/public/converted_csv/syme_oakley_syme_refs_3720.csv > /app/public/converted_csv/syme_oakley_syme_refs_3720.csv_sorted
[INFO] [2021-04-19 09:48:46] Converted: /app/public/converted_csv/syme_oakley_syme_refs_3720.csv (0 lines)
[INFO] [2021-04-19 09:48:46] ...nodes (/app/public/data/syme_oakley_syme/taxa.txt)
[CMD] [2021-04-19 09:48:46] /usr/bin/sort /app/public/converted_csv/syme_oakley_syme_nodes_3720.csv > /app/public/converted_csv/syme_oakley_syme_nodes_3720.csv_sorted
[INFO] [2021-04-19 09:48:47] Converted: /app/public/converted_csv/syme_oakley_syme_nodes_3720.csv (101 lines)
[INFO] [2021-04-19 09:48:47] ...occurrences (/app/public/data/syme_oakley_syme/occurrences.txt)
[CMD] [2021-04-19 09:48:47] /usr/bin/sort /app/public/converted_csv/syme_oakley_syme_occurrences_3720.csv > /app/public/converted_csv/syme_oakley_syme_occurrences_3720.csv_sorted
[INFO] [2021-04-19 09:48:47] Converted: /app/public/converted_csv/syme_oakley_syme_occurrences_3720.csv (101 lines)
[INFO] [2021-04-19 09:48:47] ...measurements (/app/public/data/syme_oakley_syme/measurementsorfacts.txt)
[CMD] [2021-04-19 09:48:47] /usr/bin/sort /app/public/converted_csv/syme_oakley_syme_measurements_3720.csv > /app/public/converted_csv/syme_oakley_syme_measurements_3720.csv_sorted
[INFO] [2021-04-19 09:48:48] Converted: /app/public/converted_csv/syme_oakley_syme_measurements_3720.csv (106 lines)
[STOP] [2021-04-19 09:48:48] convert_to_csv
[START] [2021-04-19 09:48:48] calculate_delta
[INFO] [2021-04-19 09:48:48] Looping over 4 formats...
[INFO] [2021-04-19 09:48:48] ...refs (/app/public/data/syme_oakley_syme/references.tsv)
[CMD] [2021-04-19 09:48:48] echo "0a" > /app/public/diff/syme_oakley_syme_refs_3720.diff
[CMD] [2021-04-19 09:48:48] tail -n +1 /app/public/converted_csv/syme_oakley_syme_refs_3720.csv >> /app/public/diff/syme_oakley_syme_refs_3720.diff
[CMD] [2021-04-19 09:48:48] echo "." >> /app/public/diff/syme_oakley_syme_refs_3720.diff
[INFO] [2021-04-19 09:48:49] Created diff: /app/public/diff/syme_oakley_syme_refs_3720.diff (2 lines)
[INFO] [2021-04-19 09:48:49] ...nodes (/app/public/data/syme_oakley_syme/taxa.txt)
[CMD] [2021-04-19 09:48:49] echo "0a" > /app/public/diff/syme_oakley_syme_nodes_3720.diff
[CMD] [2021-04-19 09:48:49] tail -n +1 /app/public/converted_csv/syme_oakley_syme_nodes_3720.csv >> /app/public/diff/syme_oakley_syme_nodes_3720.diff
[CMD] [2021-04-19 09:48:49] echo "." >> /app/public/diff/syme_oakley_syme_nodes_3720.diff
[INFO] [2021-04-19 09:48:50] Created diff: /app/public/diff/syme_oakley_syme_nodes_3720.diff (103 lines)
[INFO] [2021-04-19 09:48:50] ...occurrences (/app/public/data/syme_oakley_syme/occurrences.txt)
[CMD] [2021-04-19 09:48:50] echo "0a" > /app/public/diff/syme_oakley_syme_occurrences_3720.diff
[CMD] [2021-04-19 09:48:50] tail -n +1 /app/public/converted_csv/syme_oakley_syme_occurrences_3720.csv >> /app/public/diff/syme_oakley_syme_occurrences_3720.diff
[CMD] [2021-04-19 09:48:51] echo "." >> /app/public/diff/syme_oakley_syme_occurrences_3720.diff
[INFO] [2021-04-19 09:48:51] Created diff: /app/public/diff/syme_oakley_syme_occurrences_3720.diff (103 lines)
[INFO] [2021-04-19 09:48:51] ...measurements (/app/public/data/syme_oakley_syme/measurementsorfacts.txt)
[CMD] [2021-04-19 09:48:51] echo "0a" > /app/public/diff/syme_oakley_syme_measurements_3720.diff
[CMD] [2021-04-19 09:48:51] tail -n +1 /app/public/converted_csv/syme_oakley_syme_measurements_3720.csv >> /app/public/diff/syme_oakley_syme_measurements_3720.diff
[CMD] [2021-04-19 09:48:52] echo "." >> /app/public/diff/syme_oakley_syme_measurements_3720.diff
[INFO] [2021-04-19 09:48:52] Created diff: /app/public/diff/syme_oakley_syme_measurements_3720.diff (108 lines)
[STOP] [2021-04-19 09:48:52] calculate_delta
[START] [2021-04-19 09:48:52] parse_diff_and_store
[INFO] [2021-04-19 09:48:52] Handling diff: /app/public/diff/syme_oakley_syme_refs_3720.diff (2 lines)
[INFO] [2021-04-19 09:48:53] Loading refs diff file into memory (2 /app/public/diff/syme_oakley_syme_refs_3720.diff lines)...
[INFO] [2021-04-19 09:48:53] Handling diff: /app/public/diff/syme_oakley_syme_nodes_3720.diff (103 lines)
[INFO] [2021-04-19 09:48:53] Loading nodes diff file into memory (103 /app/public/diff/syme_oakley_syme_nodes_3720.diff lines)...
[INFO] [2021-04-19 09:48:54] Handling diff: /app/public/diff/syme_oakley_syme_occurrences_3720.diff (103 lines)
[INFO] [2021-04-19 09:48:54] Loading occurrences diff file into memory (103 /app/public/diff/syme_oakley_syme_occurrences_3720.diff lines)...
[INFO] [2021-04-19 09:48:55] Handling diff: /app/public/diff/syme_oakley_syme_measurements_3720.diff (108 lines)
[INFO] [2021-04-19 09:48:55] Loading measurements diff file into memory (108 /app/public/diff/syme_oakley_syme_measurements_3720.diff lines)...
[INFO] [2021-04-19 09:48:56] Storing 101 ScientificNames
[INFO] [2021-04-19 09:48:56] Processing group of 101 in 1 groups of 1000
[INFO] [2021-04-19 09:48:56] Average Time: 0.04
[INFO] [2021-04-19 09:48:56] Total Time: 1s
[INFO] [2021-04-19 09:48:56] Storing 101 Nodes
[INFO] [2021-04-19 09:48:56] Processing group of 101 in 1 groups of 1000
[INFO] [2021-04-19 09:48:56] Average Time: 0.05
[INFO] [2021-04-19 09:48:56] Total Time: 1s
[INFO] [2021-04-19 09:48:56] Storing 101 Occurrences
[INFO] [2021-04-19 09:48:56] Processing group of 101 in 1 groups of 1000
[INFO] [2021-04-19 09:48:56] Average Time: 0.02
[INFO] [2021-04-19 09:48:56] Total Time: 1s
[INFO] [2021-04-19 09:48:56] Storing 106 Traits
[INFO] [2021-04-19 09:48:56] Processing group of 106 in 1 groups of 1000
[INFO] [2021-04-19 09:48:56] Average Time: 0.03
[INFO] [2021-04-19 09:48:56] Total Time: 1s
[INFO] [2021-04-19 09:48:56] Storing 101 MetaTraits
[INFO] [2021-04-19 09:48:56] Processing group of 101 in 1 groups of 1000
[INFO] [2021-04-19 09:48:56] Average Time: 0.01
[INFO] [2021-04-19 09:48:56] Total Time: 1s
[STOP] [2021-04-19 09:48:56] parse_diff_and_store
[START] [2021-04-19 09:48:56] resolve_keys
[INFO] [2021-04-19 09:49:02] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 09:49:02] traits to occurrences...
[INFO] [2021-04-19 09:49:02] traits to nodes (through occurrences)...
[INFO] [2021-04-19 09:49:02] Traits to sex term...
[INFO] [2021-04-19 09:49:02] Traits to lifestage term...
[INFO] [2021-04-19 09:49:02] MetaTraits to traits...
[INFO] [2021-04-19 09:49:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 09:49:02] Assocs to occurrences...
[INFO] [2021-04-19 09:49:02] Assocs to nodes...
[INFO] [2021-04-19 09:49:02] Assoc to sex term...
[INFO] [2021-04-19 09:49:02] Assoc to lifestage term...
[INFO] [2021-04-19 09:49:02] MetaAssoc to assocs...
[STOP] [2021-04-19 09:49:02] resolve_keys
[START] [2021-04-19 09:49:02] hold_for_later_1
[STOP] [2021-04-19 09:49:02] hold_for_later_1
[START] [2021-04-19 09:49:02] hold_for_later_2
[STOP] [2021-04-19 09:49:02] hold_for_later_2
[START] [2021-04-19 09:49:02] resolve_missing_parents
[STOP] [2021-04-19 09:49:02] resolve_missing_parents
[START] [2021-04-19 09:49:02] rebuild_nodes
[START] [2021-04-19 09:49:02] Flattener#flatten
[START] [2021-04-19 09:49:02] Flattener#study_resource
[START] [2021-04-19 09:49:02] Flattener#build_ancestry
[STOP] [2021-04-19 09:49:02] Flattener#build_ancestry
[INFO] [2021-04-19 09:49:02] 101 ancestry keys
[START] [2021-04-19 09:49:02] build_node_ancestors
[INFO] [2021-04-19 09:49:02] old ancestors deleted.
[STOP] [2021-04-19 09:49:02] build_node_ancestors
[WARN] [2021-04-19 09:49:02] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 09:49:02] Flattener#flatten
[STOP] [2021-04-19 09:49:02] rebuild_nodes
[START] [2021-04-19 09:49:02] resolve_missing_media_owners
[STOP] [2021-04-19 09:49:02] resolve_missing_media_owners
[START] [2021-04-19 09:49:02] sanitize_media_verbatims
[STOP] [2021-04-19 09:49:02] sanitize_media_verbatims
[START] [2021-04-19 09:49:02] queue_downloads
[STOP] [2021-04-19 09:49:02] queue_downloads
[START] [2021-04-19 09:49:02] parse_names
[WARN] [2021-04-19 09:49:02] I see 101 names which still need to be parsed.
[STOP] [2021-04-19 09:49:03] parse_names
[START] [2021-04-19 09:49:03] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 09:49:03] denormalize_canonical_names_to_nodes
[START] [2021-04-19 09:49:03] match_nodes
[START] [2021-04-19 09:49:03] map_all_nodes_to_pages
[STOP] [2021-04-19 09:49:03] map_all_nodes_to_pages
[INFO] [2021-04-19 09:49:03] ZERO unmatched nodes (of 101)! Nicely done.
[START] [2021-04-19 09:49:03] update_nodes
[STOP] [2021-04-19 09:49:03] update_nodes
[STOP] [2021-04-19 09:49:03] match_nodes
[START] [2021-04-19 09:49:03] reindex_search
[STOP] [2021-04-19 09:49:03] reindex_search
[START] [2021-04-19 09:49:03] normalize_units
[STOP] [2021-04-19 09:49:03] normalize_units
[START] [2021-04-19 09:49:03] calculate_statistics
[2021-04-19 09:49:03] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 09:49:03] calculate_statistics
[START] [2021-04-19 09:49:03] complete_harvest_instance
[START] [2021-04-19 09:49:03] overall_tsv_creation
[INFO] [2021-04-19 09:49:03] Processing group of 101 in 1 batches of 10000
[INFO] [2021-04-19 09:49:40] 101 Traits (unfiltered)...
[INFO] [2021-04-19 09:50:15] 101 Traits (filtered)...
[INFO] [2021-04-19 09:50:15] 0 Associations (filtered)...
[INFO] [2021-04-19 09:50:15] 5 metadata added.
[INFO] [2021-04-19 09:50:15] 0 metadata added.
[INFO] [2021-04-19 09:50:43] Average Time: 74.51
[INFO] [2021-04-19 09:50:43] Total Time: 1m40s
[STOP] [2021-04-19 09:50:43] overall_tsv_creation
[INFO] [2021-04-19 09:50:43] Done. Check your files:
[INFO] [2021-04-19 09:50:43] (101 lines) /app/public/data/syme_oakley_syme/publish_nodes.tsv
[INFO] [2021-04-19 09:50:43] (101 lines) /app/public/data/syme_oakley_syme/publish_scientific_names.tsv
[INFO] [2021-04-19 09:50:44] (102 lines) /app/public/data/syme_oakley_syme/publish_traits.tsv
[INFO] [2021-04-19 09:50:44] (6 lines) /app/public/data/syme_oakley_syme/publish_metadata.tsv
[STOP] [2021-04-19 09:50:44] complete_harvest_instance
[START] [2021-04-19 09:50:44] completed
[STOP] [2021-04-19 09:50:44] completed
[STOP] [2021-04-19 09:50:44] logged process, took 118.65

Latest Process

19 Apr 09:48 EXITED currently processing 0