Stage:
completed
Fetched:
01 Apr 13:37
Validated:
01 Apr 13:37
Deltas Created
01 Apr 13:37
Units Normalized:
01 Apr 13:37
Ancestry Built:
01 Apr 13:37
Nodes Matched:
01 Apr 13:37
Names Parsed:
01 Apr 13:37
New Models Stored:
01 Apr 13:37
Indexed:
01 Apr 13:37
Completed:
01 Apr 13:39
Time to Harvest:
less than a minute
Harvesting Log
(738 lines)
# Logfile created on 2021-02-03 10:54:32 -0500 by logger.rb/v1.4.2
[START] [2021-02-03 10:54:33] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 10:54:33] Creating resource from OpenData
[START] [2021-02-03 10:54:33] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 10:54:33] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 10:54:33] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 10:54:33] Creating resource from OpenData
[INFO] [2021-02-03 10:55:09] ## HARVEST: type = -harvest
[START] [2021-02-03 10:55:12] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 10:55:12] create_harvest_instance
[STOP] [2021-02-03 10:55:14] create_harvest_instance
[START] [2021-02-03 10:55:14] fetch_files
[STOP] [2021-02-03 10:55:14] fetch_files
[START] [2021-02-03 10:55:14] validate_each_file
[STOP] [2021-02-03 10:55:14] validate_each_file
[START] [2021-02-03 10:55:14] convert_to_csv
[CMD] [2021-02-03 10:55:14] /usr/bin/sort /app/public/converted_csv/lewis_taylor_lew_nodes_26608.csv > /app/public/converted_csv/lewis_taylor_lew_nodes_26608.csv_sorted
[CMD] [2021-02-03 10:55:14] /usr/bin/sort /app/public/converted_csv/lewis_taylor_lew_occurrences_26609.csv > /app/public/converted_csv/lewis_taylor_lew_occurrences_26609.csv_sorted
[CMD] [2021-02-03 10:55:14] /usr/bin/sort /app/public/converted_csv/lewis_taylor_lew_measurements_26610.csv > /app/public/converted_csv/lewis_taylor_lew_measurements_26610.csv_sorted
[STOP] [2021-02-03 10:55:14] convert_to_csv
[START] [2021-02-03 10:55:14] calculate_delta
[CMD] [2021-02-03 10:55:14] echo "0a" > /app/public/diff/lewis_taylor_lew_nodes_26608.diff
[CMD] [2021-02-03 10:55:14] tail -n +1 /app/public/converted_csv/lewis_taylor_lew_nodes_26608.csv >> /app/public/diff/lewis_taylor_lew_nodes_26608.diff
[CMD] [2021-02-03 10:55:14] echo "." >> /app/public/diff/lewis_taylor_lew_nodes_26608.diff
[CMD] [2021-02-03 10:55:14] echo "0a" > /app/public/diff/lewis_taylor_lew_occurrences_26609.diff
[CMD] [2021-02-03 10:55:14] tail -n +1 /app/public/converted_csv/lewis_taylor_lew_occurrences_26609.csv >> /app/public/diff/lewis_taylor_lew_occurrences_26609.diff
[CMD] [2021-02-03 10:55:14] echo "." >> /app/public/diff/lewis_taylor_lew_occurrences_26609.diff
[CMD] [2021-02-03 10:55:14] echo "0a" > /app/public/diff/lewis_taylor_lew_measurements_26610.diff
[CMD] [2021-02-03 10:55:14] tail -n +1 /app/public/converted_csv/lewis_taylor_lew_measurements_26610.csv >> /app/public/diff/lewis_taylor_lew_measurements_26610.diff
[CMD] [2021-02-03 10:55:14] echo "." >> /app/public/diff/lewis_taylor_lew_measurements_26610.diff
[STOP] [2021-02-03 10:55:14] calculate_delta
[START] [2021-02-03 10:55:14] parse_diff_and_store
[INFO] [2021-02-03 10:55:14] Loading nodes diff file into memory (true lines)...
[INFO] [2021-02-03 10:55:14] Loading occurrences diff file into memory (true lines)...
[INFO] [2021-02-03 10:55:15] Loading measurements diff file into memory (true lines)...
[INFO] [2021-02-03 10:55:15] Storing 10 ScientificNames
[INFO] [2021-02-03 10:55:15] Processing group of 10 in 1 groups of 1000
[INFO] [2021-02-03 10:55:15] Average Time: 0.01
[INFO] [2021-02-03 10:55:15] Total Time: 1s
[INFO] [2021-02-03 10:55:15] Storing 10 Nodes
[INFO] [2021-02-03 10:55:15] Processing group of 10 in 1 groups of 1000
[INFO] [2021-02-03 10:55:15] Average Time: 0.0
[INFO] [2021-02-03 10:55:15] Total Time: 1s
[INFO] [2021-02-03 10:55:15] Storing 10 Occurrences
[INFO] [2021-02-03 10:55:15] Processing group of 10 in 1 groups of 1000
[INFO] [2021-02-03 10:55:15] Average Time: 0.0
[INFO] [2021-02-03 10:55:15] Total Time: 1s
[INFO] [2021-02-03 10:55:15] Storing 10 OccurrenceMetadata
[INFO] [2021-02-03 10:55:15] Processing group of 10 in 1 groups of 1000
[INFO] [2021-02-03 10:55:15] Average Time: 0.0
[INFO] [2021-02-03 10:55:15] Total Time: 1s
[INFO] [2021-02-03 10:55:15] Storing 39 Traits
[INFO] [2021-02-03 10:55:15] Processing group of 39 in 1 groups of 1000
[INFO] [2021-02-03 10:55:15] Average Time: 0.02
[INFO] [2021-02-03 10:55:15] Total Time: 1s
[INFO] [2021-02-03 10:55:15] Storing 20 MetaTraits
[INFO] [2021-02-03 10:55:15] Processing group of 20 in 1 groups of 1000
[INFO] [2021-02-03 10:55:15] Average Time: 0.0
[INFO] [2021-02-03 10:55:15] Total Time: 1s
[STOP] [2021-02-03 10:55:15] parse_diff_and_store
[START] [2021-02-03 10:55:15] resolve_keys
[INFO] [2021-02-03 10:55:21] Occurrences to nodes (through scientific_names)...
[INFO] [2021-02-03 10:55:21] traits to occurrences...
[INFO] [2021-02-03 10:55:21] traits to nodes (through occurrences)...
[INFO] [2021-02-03 10:55:21] Traits to sex term...
[INFO] [2021-02-03 10:55:21] Traits to lifestage term...
[INFO] [2021-02-03 10:55:21] MetaTraits to traits...
[INFO] [2021-02-03 10:55:21] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-02-03 10:55:21] Assocs to occurrences...
[INFO] [2021-02-03 10:55:21] Assocs to nodes...
[INFO] [2021-02-03 10:55:21] Assoc to sex term...
[INFO] [2021-02-03 10:55:21] Assoc to lifestage term...
[INFO] [2021-02-03 10:55:21] MetaAssoc to assocs...
[STOP] [2021-02-03 10:55:21] resolve_keys
[START] [2021-02-03 10:55:21] hold_for_later_1
[STOP] [2021-02-03 10:55:21] hold_for_later_1
[START] [2021-02-03 10:55:21] hold_for_later_2
[STOP] [2021-02-03 10:55:21] hold_for_later_2
[START] [2021-02-03 10:55:21] resolve_missing_parents
[STOP] [2021-02-03 10:55:21] resolve_missing_parents
[START] [2021-02-03 10:55:21] rebuild_nodes
[START] [2021-02-03 10:55:21] Flattener#flatten
[START] [2021-02-03 10:55:21] Flattener#study_resource
[START] [2021-02-03 10:55:21] Flattener#build_ancestry
[STOP] [2021-02-03 10:55:21] Flattener#build_ancestry
[INFO] [2021-02-03 10:55:21] 10 ancestry keys
[START] [2021-02-03 10:55:21] build_node_ancestors
[INFO] [2021-02-03 10:55:21] old ancestors deleted.
[STOP] [2021-02-03 10:55:21] build_node_ancestors
[WARN] [2021-02-03 10:55:21] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-02-03 10:55:21] Flattener#flatten
[STOP] [2021-02-03 10:55:21] rebuild_nodes
[START] [2021-02-03 10:55:21] resolve_missing_media_owners
[STOP] [2021-02-03 10:55:21] resolve_missing_media_owners
[START] [2021-02-03 10:55:21] sanitize_media_verbatims
[STOP] [2021-02-03 10:55:21] sanitize_media_verbatims
[START] [2021-02-03 10:55:21] queue_downloads
[STOP] [2021-02-03 10:55:21] queue_downloads
[START] [2021-02-03 10:55:21] parse_names
[WARN] [2021-02-03 10:55:21] I see 10 names which still need to be parsed.
[STOP] [2021-02-03 10:55:22] parse_names
[START] [2021-02-03 10:55:22] denormalize_canonical_names_to_nodes
[STOP] [2021-02-03 10:55:22] denormalize_canonical_names_to_nodes
[START] [2021-02-03 10:55:22] match_nodes
[START] [2021-02-03 10:55:22] map_all_nodes_to_pages
[STOP] [2021-02-03 10:55:22] map_all_nodes_to_pages
[INFO] [2021-02-03 10:55:22] ZERO unmatched nodes (of 10)! Nicely done.
[START] [2021-02-03 10:55:22] update_nodes
[STOP] [2021-02-03 10:55:22] update_nodes
[STOP] [2021-02-03 10:55:22] match_nodes
[START] [2021-02-03 10:55:22] reindex_search
[STOP] [2021-02-03 10:55:22] reindex_search
[START] [2021-02-03 10:55:22] normalize_units
[STOP] [2021-02-03 10:55:22] normalize_units
[START] [2021-02-03 10:55:22] calculate_statistics
[2021-02-03 10:55:22] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-02-03 10:55:22] calculate_statistics
[START] [2021-02-03 10:55:22] complete_harvest_instance
[START] [2021-02-03 10:55:22] overall_tsv_creation
[INFO] [2021-02-03 10:55:23] Processing group of 10 in 1 batches of 10000
[INFO] [2021-02-03 10:56:02] 10 Traits (unfiltered)...
[INFO] [2021-02-03 10:56:38] 10 Traits (filtered)...
[INFO] [2021-02-03 10:56:38] 0 Associations (filtered)...
[INFO] [2021-02-03 10:56:38] 49 metadata added.
[INFO] [2021-02-03 10:56:38] 0 metadata added.
[INFO] [2021-02-03 10:57:10] Average Time: 81.18
[INFO] [2021-02-03 10:57:10] Total Time: 1m48s
[STOP] [2021-02-03 10:57:10] overall_tsv_creation
[INFO] [2021-02-03 10:57:10] Done. Check your files:
[INFO] [2021-02-03 10:57:10] (10 lines) /app/public/data/lewis_taylor_lew/publish_nodes.tsv
[INFO] [2021-02-03 10:57:10] (10 lines) /app/public/data/lewis_taylor_lew/publish_scientific_names.tsv
[INFO] [2021-02-03 10:57:10] (11 lines) /app/public/data/lewis_taylor_lew/publish_traits.tsv
[INFO] [2021-02-03 10:57:10] (50 lines) /app/public/data/lewis_taylor_lew/publish_metadata.tsv
[STOP] [2021-02-03 10:57:10] complete_harvest_instance
[START] [2021-02-03 10:57:10] completed
[STOP] [2021-02-03 10:57:10] completed
[STOP] [2021-02-03 10:57:10] logged process, took 117.25
[INFO] [2021-02-03 11:02:43] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-02-03 11:02:46] ## remove_type: ScientificName
[INFO] [2021-02-03 11:02:46] ++ Calling delete_all on 10 instances...
[INFO] [2021-02-03 11:02:46] [11:02:46.361] Removed 10 Scientificnames
[INFO] [2021-02-03 11:02:46] ## remove_type: Vernacular
[INFO] [2021-02-03 11:02:46] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:02:46] [11:02:46.364] Removed 0 Vernaculars
[INFO] [2021-02-03 11:02:46] ## remove_type: Article
[INFO] [2021-02-03 11:02:46] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:02:46] [11:02:46.367] Removed 0 Articles
[INFO] [2021-02-03 11:02:46] ## remove_type: Medium
[INFO] [2021-02-03 11:02:46] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:02:46] [11:02:46.371] Removed 0 Media
[INFO] [2021-02-03 11:02:46] ## remove_type: Trait
[INFO] [2021-02-03 11:02:46] ++ Calling delete_all on 39 instances...
[INFO] [2021-02-03 11:02:46] [11:02:46.376] Removed 39 Traits
[INFO] [2021-02-03 11:02:46] ## remove_type: MetaTrait
[INFO] [2021-02-03 11:02:46] ++ Calling delete_all on 20 instances...
[INFO] [2021-02-03 11:02:46] [11:02:46.379] Removed 20 Metatraits
[INFO] [2021-02-03 11:02:46] ## remove_type: OccurrenceMetadatum
[INFO] [2021-02-03 11:02:46] ++ Calling delete_all on 10 instances...
[INFO] [2021-02-03 11:02:46] [11:02:46.382] Removed 10 Occurrencemetadata
[INFO] [2021-02-03 11:02:46] ## remove_type: Assoc
[INFO] [2021-02-03 11:02:46] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:02:46] [11:02:46.385] Removed 0 Assocs
[INFO] [2021-02-03 11:02:46] ## remove_type: MetaAssoc
[INFO] [2021-02-03 11:02:46] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:02:46] [11:02:46.387] Removed 0 Metaassocs
[INFO] [2021-02-03 11:02:46] ## remove_type: Identifier
[INFO] [2021-02-03 11:02:46] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:02:46] [11:02:46.389] Removed 0 Identifiers
[INFO] [2021-02-03 11:02:46] ## remove_type: Reference
[INFO] [2021-02-03 11:02:46] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:02:46] [11:02:46.392] Removed 0 References
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728787...
[INFO] [2021-02-03 11:02:46] Starting batch with ID 87728780...
[INFO] [2021-02-03 11:02:46] ## remove_type: Node
[INFO] [2021-02-03 11:02:46] ++ Calling delete_all on 10 instances...
[INFO] [2021-02-03 11:02:46] [11:02:46.994] Removed 10 Nodes
[START] [2021-02-03 11:02:47] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 11:02:47] Creating resource from OpenData
[START] [2021-02-03 11:02:47] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 11:02:47] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:02:47] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:02:47] Creating resource from OpenData
[START] [2021-02-03 11:02:47] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 11:02:47] create_harvest_instance
[STOP] [2021-02-03 11:02:49] create_harvest_instance
[START] [2021-02-03 11:02:49] fetch_files
[STOP] [2021-02-03 11:02:49] fetch_files
[START] [2021-02-03 11:02:49] validate_each_file
[STOP] [2021-02-03 11:02:49] validate_each_file
[START] [2021-02-03 11:02:49] convert_to_csv
[CMD] [2021-02-03 11:02:49] /usr/bin/sort /app/public/converted_csv/lewis_taylor_lew_nodes_26626.csv > /app/public/converted_csv/lewis_taylor_lew_nodes_26626.csv_sorted
[CMD] [2021-02-03 11:02:49] /usr/bin/sort /app/public/converted_csv/lewis_taylor_lew_occurrences_26627.csv > /app/public/converted_csv/lewis_taylor_lew_occurrences_26627.csv_sorted
[CMD] [2021-02-03 11:02:49] /usr/bin/sort /app/public/converted_csv/lewis_taylor_lew_measurements_26628.csv > /app/public/converted_csv/lewis_taylor_lew_measurements_26628.csv_sorted
[STOP] [2021-02-03 11:02:49] convert_to_csv
[START] [2021-02-03 11:02:49] calculate_delta
[CMD] [2021-02-03 11:02:49] echo "0a" > /app/public/diff/lewis_taylor_lew_nodes_26626.diff
[CMD] [2021-02-03 11:02:49] tail -n +1 /app/public/converted_csv/lewis_taylor_lew_nodes_26626.csv >> /app/public/diff/lewis_taylor_lew_nodes_26626.diff
[CMD] [2021-02-03 11:02:49] echo "." >> /app/public/diff/lewis_taylor_lew_nodes_26626.diff
[CMD] [2021-02-03 11:02:49] echo "0a" > /app/public/diff/lewis_taylor_lew_occurrences_26627.diff
[CMD] [2021-02-03 11:02:49] tail -n +1 /app/public/converted_csv/lewis_taylor_lew_occurrences_26627.csv >> /app/public/diff/lewis_taylor_lew_occurrences_26627.diff
[CMD] [2021-02-03 11:02:49] echo "." >> /app/public/diff/lewis_taylor_lew_occurrences_26627.diff
[CMD] [2021-02-03 11:02:49] echo "0a" > /app/public/diff/lewis_taylor_lew_measurements_26628.diff
[CMD] [2021-02-03 11:02:49] tail -n +1 /app/public/converted_csv/lewis_taylor_lew_measurements_26628.csv >> /app/public/diff/lewis_taylor_lew_measurements_26628.diff
[CMD] [2021-02-03 11:02:49] echo "." >> /app/public/diff/lewis_taylor_lew_measurements_26628.diff
[STOP] [2021-02-03 11:02:49] calculate_delta
[START] [2021-02-03 11:02:49] parse_diff_and_store
[INFO] [2021-02-03 11:02:49] Loading nodes diff file into memory (true lines)...
[INFO] [2021-02-03 11:02:49] Loading occurrences diff file into memory (true lines)...
[INFO] [2021-02-03 11:02:50] Loading measurements diff file into memory (true lines)...
[INFO] [2021-02-03 11:02:50] Storing 10 ScientificNames
[INFO] [2021-02-03 11:02:50] Processing group of 10 in 1 groups of 1000
[INFO] [2021-02-03 11:02:50] Average Time: 0.0
[INFO] [2021-02-03 11:02:50] Total Time: 1s
[INFO] [2021-02-03 11:02:50] Storing 10 Nodes
[INFO] [2021-02-03 11:02:50] Processing group of 10 in 1 groups of 1000
[INFO] [2021-02-03 11:02:50] Average Time: 0.0
[INFO] [2021-02-03 11:02:50] Total Time: 1s
[INFO] [2021-02-03 11:02:50] Storing 10 Occurrences
[INFO] [2021-02-03 11:02:50] Processing group of 10 in 1 groups of 1000
[INFO] [2021-02-03 11:02:50] Average Time: 0.0
[INFO] [2021-02-03 11:02:50] Total Time: 1s
[INFO] [2021-02-03 11:02:50] Storing 10 OccurrenceMetadata
[INFO] [2021-02-03 11:02:50] Processing group of 10 in 1 groups of 1000
[INFO] [2021-02-03 11:02:50] Average Time: 0.0
[INFO] [2021-02-03 11:02:50] Total Time: 1s
[INFO] [2021-02-03 11:02:50] Storing 39 Traits
[INFO] [2021-02-03 11:02:50] Processing group of 39 in 1 groups of 1000
[INFO] [2021-02-03 11:02:50] Average Time: 0.01
[INFO] [2021-02-03 11:02:50] Total Time: 1s
[INFO] [2021-02-03 11:02:50] Storing 20 MetaTraits
[INFO] [2021-02-03 11:02:50] Processing group of 20 in 1 groups of 1000
[INFO] [2021-02-03 11:02:50] Average Time: 0.01
[INFO] [2021-02-03 11:02:50] Total Time: 1s
[STOP] [2021-02-03 11:02:50] parse_diff_and_store
[START] [2021-02-03 11:02:50] resolve_keys
[INFO] [2021-02-03 11:02:56] Occurrences to nodes (through scientific_names)...
[INFO] [2021-02-03 11:02:56] traits to occurrences...
[INFO] [2021-02-03 11:02:56] traits to nodes (through occurrences)...
[INFO] [2021-02-03 11:02:56] Traits to sex term...
[INFO] [2021-02-03 11:02:56] Traits to lifestage term...
[INFO] [2021-02-03 11:02:56] MetaTraits to traits...
[INFO] [2021-02-03 11:02:56] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-02-03 11:02:56] Assocs to occurrences...
[INFO] [2021-02-03 11:02:56] Assocs to nodes...
[INFO] [2021-02-03 11:02:56] Assoc to sex term...
[INFO] [2021-02-03 11:02:56] Assoc to lifestage term...
[INFO] [2021-02-03 11:02:56] MetaAssoc to assocs...
[STOP] [2021-02-03 11:02:56] resolve_keys
[START] [2021-02-03 11:02:56] hold_for_later_1
[STOP] [2021-02-03 11:02:56] hold_for_later_1
[START] [2021-02-03 11:02:56] hold_for_later_2
[STOP] [2021-02-03 11:02:56] hold_for_later_2
[START] [2021-02-03 11:02:56] resolve_missing_parents
[STOP] [2021-02-03 11:02:56] resolve_missing_parents
[START] [2021-02-03 11:02:56] rebuild_nodes
[START] [2021-02-03 11:02:56] Flattener#flatten
[START] [2021-02-03 11:02:56] Flattener#study_resource
[START] [2021-02-03 11:02:56] Flattener#build_ancestry
[STOP] [2021-02-03 11:02:56] Flattener#build_ancestry
[INFO] [2021-02-03 11:02:56] 10 ancestry keys
[START] [2021-02-03 11:02:56] build_node_ancestors
[INFO] [2021-02-03 11:02:56] old ancestors deleted.
[STOP] [2021-02-03 11:02:56] build_node_ancestors
[WARN] [2021-02-03 11:02:56] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-02-03 11:02:56] Flattener#flatten
[STOP] [2021-02-03 11:02:56] rebuild_nodes
[START] [2021-02-03 11:02:56] resolve_missing_media_owners
[STOP] [2021-02-03 11:02:56] resolve_missing_media_owners
[START] [2021-02-03 11:02:56] sanitize_media_verbatims
[STOP] [2021-02-03 11:02:56] sanitize_media_verbatims
[START] [2021-02-03 11:02:56] queue_downloads
[STOP] [2021-02-03 11:02:56] queue_downloads
[START] [2021-02-03 11:02:56] parse_names
[WARN] [2021-02-03 11:02:56] I see 10 names which still need to be parsed.
[STOP] [2021-02-03 11:02:57] parse_names
[START] [2021-02-03 11:02:57] denormalize_canonical_names_to_nodes
[STOP] [2021-02-03 11:02:57] denormalize_canonical_names_to_nodes
[START] [2021-02-03 11:02:57] match_nodes
[START] [2021-02-03 11:02:57] map_all_nodes_to_pages
[STOP] [2021-02-03 11:02:57] map_all_nodes_to_pages
[INFO] [2021-02-03 11:02:57] ZERO unmatched nodes (of 10)! Nicely done.
[START] [2021-02-03 11:02:57] update_nodes
[STOP] [2021-02-03 11:02:57] update_nodes
[STOP] [2021-02-03 11:02:57] match_nodes
[START] [2021-02-03 11:02:57] reindex_search
[STOP] [2021-02-03 11:02:57] reindex_search
[START] [2021-02-03 11:02:57] normalize_units
[STOP] [2021-02-03 11:02:57] normalize_units
[START] [2021-02-03 11:02:57] calculate_statistics
[2021-02-03 11:02:57] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-02-03 11:02:57] calculate_statistics
[START] [2021-02-03 11:02:57] complete_harvest_instance
[START] [2021-02-03 11:02:57] overall_tsv_creation
[INFO] [2021-02-03 11:02:57] Processing group of 10 in 1 batches of 10000
[INFO] [2021-02-03 11:03:36] 10 Traits (unfiltered)...
[INFO] [2021-02-03 11:04:12] 10 Traits (filtered)...
[INFO] [2021-02-03 11:04:12] 0 Associations (filtered)...
[INFO] [2021-02-03 11:04:12] 49 metadata added.
[INFO] [2021-02-03 11:04:12] 0 metadata added.
[INFO] [2021-02-03 11:04:43] Average Time: 80.76
[INFO] [2021-02-03 11:04:43] Total Time: 1m47s
[STOP] [2021-02-03 11:04:43] overall_tsv_creation
[INFO] [2021-02-03 11:04:43] Done. Check your files:
[INFO] [2021-02-03 11:04:43] (10 lines) /app/public/data/lewis_taylor_lew/publish_nodes.tsv
[INFO] [2021-02-03 11:04:43] (10 lines) /app/public/data/lewis_taylor_lew/publish_scientific_names.tsv
[INFO] [2021-02-03 11:04:43] (11 lines) /app/public/data/lewis_taylor_lew/publish_traits.tsv
[INFO] [2021-02-03 11:04:43] (50 lines) /app/public/data/lewis_taylor_lew/publish_metadata.tsv
[STOP] [2021-02-03 11:04:43] complete_harvest_instance
[START] [2021-02-03 11:04:43] completed
[STOP] [2021-02-03 11:04:43] completed
[STOP] [2021-02-03 11:04:43] logged process, took 116.31
[INFO] [2021-02-03 11:27:20] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-02-03 11:27:22] ## remove_type: ScientificName
[INFO] [2021-02-03 11:27:22] ++ Calling delete_all on 10 instances...
[INFO] [2021-02-03 11:27:22] [11:27:22.765] Removed 10 Scientificnames
[INFO] [2021-02-03 11:27:22] ## remove_type: Vernacular
[INFO] [2021-02-03 11:27:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:27:22] [11:27:22.767] Removed 0 Vernaculars
[INFO] [2021-02-03 11:27:22] ## remove_type: Article
[INFO] [2021-02-03 11:27:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:27:22] [11:27:22.771] Removed 0 Articles
[INFO] [2021-02-03 11:27:22] ## remove_type: Medium
[INFO] [2021-02-03 11:27:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:27:22] [11:27:22.775] Removed 0 Media
[INFO] [2021-02-03 11:27:22] ## remove_type: Trait
[INFO] [2021-02-03 11:27:22] ++ Calling delete_all on 39 instances...
[INFO] [2021-02-03 11:27:22] [11:27:22.781] Removed 39 Traits
[INFO] [2021-02-03 11:27:22] ## remove_type: MetaTrait
[INFO] [2021-02-03 11:27:22] ++ Calling delete_all on 20 instances...
[INFO] [2021-02-03 11:27:22] [11:27:22.784] Removed 20 Metatraits
[INFO] [2021-02-03 11:27:22] ## remove_type: OccurrenceMetadatum
[INFO] [2021-02-03 11:27:22] ++ Calling delete_all on 10 instances...
[INFO] [2021-02-03 11:27:22] [11:27:22.788] Removed 10 Occurrencemetadata
[INFO] [2021-02-03 11:27:22] ## remove_type: Assoc
[INFO] [2021-02-03 11:27:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:27:22] [11:27:22.791] Removed 0 Assocs
[INFO] [2021-02-03 11:27:22] ## remove_type: MetaAssoc
[INFO] [2021-02-03 11:27:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:27:22] [11:27:22.793] Removed 0 Metaassocs
[INFO] [2021-02-03 11:27:22] ## remove_type: Identifier
[INFO] [2021-02-03 11:27:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:27:22] [11:27:22.795] Removed 0 Identifiers
[INFO] [2021-02-03 11:27:22] ## remove_type: Reference
[INFO] [2021-02-03 11:27:22] ++ Calling delete_all on 0 instances...
[INFO] [2021-02-03 11:27:22] [11:27:22.797] Removed 0 References
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:22] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:23] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:23] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:23] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:23] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:23] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:23] Starting batch with ID 87728803...
[INFO] [2021-02-03 11:27:23] ## remove_type: Node
[INFO] [2021-02-03 11:27:23] ++ Calling delete_all on 10 instances...
[INFO] [2021-02-03 11:27:23] [11:27:23.397] Removed 10 Nodes
[START] [2021-02-03 11:27:23] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 11:27:23] Creating resource from OpenData
[START] [2021-02-03 11:27:23] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 11:27:23] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:27:24] Parse meta.xml file and create formats with fields
[STOP] [2021-02-03 11:27:24] Creating resource from OpenData
[START] [2021-02-03 11:27:24] logged process: 16b22834be7ac1492cba86047bb0f5dbfa370977
[START] [2021-02-03 11:27:24] create_harvest_instance
[STOP] [2021-02-03 11:27:25] create_harvest_instance
[START] [2021-02-03 11:27:25] fetch_files
[STOP] [2021-02-03 11:27:25] fetch_files
[START] [2021-02-03 11:27:25] validate_each_file
[STOP] [2021-02-03 11:27:25] validate_each_file
[START] [2021-02-03 11:27:25] convert_to_csv
[CMD] [2021-02-03 11:27:25] /usr/bin/sort /app/public/converted_csv/lewis_taylor_lew_nodes_26671.csv > /app/public/converted_csv/lewis_taylor_lew_nodes_26671.csv_sorted
[CMD] [2021-02-03 11:27:25] /usr/bin/sort /app/public/converted_csv/lewis_taylor_lew_occurrences_26672.csv > /app/public/converted_csv/lewis_taylor_lew_occurrences_26672.csv_sorted
[CMD] [2021-02-03 11:27:25] /usr/bin/sort /app/public/converted_csv/lewis_taylor_lew_measurements_26673.csv > /app/public/converted_csv/lewis_taylor_lew_measurements_26673.csv_sorted
[STOP] [2021-02-03 11:27:25] convert_to_csv
[START] [2021-02-03 11:27:25] calculate_delta
[CMD] [2021-02-03 11:27:25] echo "0a" > /app/public/diff/lewis_taylor_lew_nodes_26671.diff
[CMD] [2021-02-03 11:27:25] tail -n +1 /app/public/converted_csv/lewis_taylor_lew_nodes_26671.csv >> /app/public/diff/lewis_taylor_lew_nodes_26671.diff
[CMD] [2021-02-03 11:27:25] echo "." >> /app/public/diff/lewis_taylor_lew_nodes_26671.diff
[CMD] [2021-02-03 11:27:25] echo "0a" > /app/public/diff/lewis_taylor_lew_occurrences_26672.diff
[CMD] [2021-02-03 11:27:25] tail -n +1 /app/public/converted_csv/lewis_taylor_lew_occurrences_26672.csv >> /app/public/diff/lewis_taylor_lew_occurrences_26672.diff
[CMD] [2021-02-03 11:27:25] echo "." >> /app/public/diff/lewis_taylor_lew_occurrences_26672.diff
[CMD] [2021-02-03 11:27:25] echo "0a" > /app/public/diff/lewis_taylor_lew_measurements_26673.diff
[CMD] [2021-02-03 11:27:25] tail -n +1 /app/public/converted_csv/lewis_taylor_lew_measurements_26673.csv >> /app/public/diff/lewis_taylor_lew_measurements_26673.diff
[CMD] [2021-02-03 11:27:25] echo "." >> /app/public/diff/lewis_taylor_lew_measurements_26673.diff
[STOP] [2021-02-03 11:27:25] calculate_delta
[START] [2021-02-03 11:27:25] parse_diff_and_store
[INFO] [2021-02-03 11:27:25] Loading nodes diff file into memory (true lines)...
[INFO] [2021-02-03 11:27:25] Loading occurrences diff file into memory (true lines)...
[INFO] [2021-02-03 11:27:26] Loading measurements diff file into memory (true lines)...
[INFO] [2021-02-03 11:27:26] Storing 10 ScientificNames
[INFO] [2021-02-03 11:27:26] Processing group of 10 in 1 groups of 1000
[INFO] [2021-02-03 11:27:26] Average Time: 0.01
[INFO] [2021-02-03 11:27:26] Total Time: 1s
[INFO] [2021-02-03 11:27:26] Storing 10 Nodes
[INFO] [2021-02-03 11:27:26] Processing group of 10 in 1 groups of 1000
[INFO] [2021-02-03 11:27:26] Average Time: 0.0
[INFO] [2021-02-03 11:27:26] Total Time: 1s
[INFO] [2021-02-03 11:27:26] Storing 10 Occurrences
[INFO] [2021-02-03 11:27:26] Processing group of 10 in 1 groups of 1000
[INFO] [2021-02-03 11:27:26] Average Time: 0.0
[INFO] [2021-02-03 11:27:26] Total Time: 1s
[INFO] [2021-02-03 11:27:26] Storing 10 OccurrenceMetadata
[INFO] [2021-02-03 11:27:26] Processing group of 10 in 1 groups of 1000
[INFO] [2021-02-03 11:27:26] Average Time: 0.0
[INFO] [2021-02-03 11:27:26] Total Time: 1s
[INFO] [2021-02-03 11:27:26] Storing 40 Traits
[INFO] [2021-02-03 11:27:26] Processing group of 40 in 1 groups of 1000
[INFO] [2021-02-03 11:27:26] Average Time: 0.01
[INFO] [2021-02-03 11:27:26] Total Time: 1s
[INFO] [2021-02-03 11:27:26] Storing 20 MetaTraits
[INFO] [2021-02-03 11:27:26] Processing group of 20 in 1 groups of 1000
[INFO] [2021-02-03 11:27:26] Average Time: 0.0
[INFO] [2021-02-03 11:27:26] Total Time: 1s
[STOP] [2021-02-03 11:27:26] parse_diff_and_store
[START] [2021-02-03 11:27:26] resolve_keys
[INFO] [2021-02-03 11:27:32] Occurrences to nodes (through scientific_names)...
[INFO] [2021-02-03 11:27:32] traits to occurrences...
[INFO] [2021-02-03 11:27:32] traits to nodes (through occurrences)...
[INFO] [2021-02-03 11:27:32] Traits to sex term...
[INFO] [2021-02-03 11:27:32] Traits to lifestage term...
[INFO] [2021-02-03 11:27:32] MetaTraits to traits...
[INFO] [2021-02-03 11:27:32] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-02-03 11:27:32] Assocs to occurrences...
[INFO] [2021-02-03 11:27:32] Assocs to nodes...
[INFO] [2021-02-03 11:27:32] Assoc to sex term...
[INFO] [2021-02-03 11:27:32] Assoc to lifestage term...
[INFO] [2021-02-03 11:27:32] MetaAssoc to assocs...
[STOP] [2021-02-03 11:27:32] resolve_keys
[START] [2021-02-03 11:27:32] hold_for_later_1
[STOP] [2021-02-03 11:27:32] hold_for_later_1
[START] [2021-02-03 11:27:32] hold_for_later_2
[STOP] [2021-02-03 11:27:32] hold_for_later_2
[START] [2021-02-03 11:27:32] resolve_missing_parents
[STOP] [2021-02-03 11:27:32] resolve_missing_parents
[START] [2021-02-03 11:27:32] rebuild_nodes
[START] [2021-02-03 11:27:32] Flattener#flatten
[START] [2021-02-03 11:27:32] Flattener#study_resource
[START] [2021-02-03 11:27:32] Flattener#build_ancestry
[STOP] [2021-02-03 11:27:32] Flattener#build_ancestry
[INFO] [2021-02-03 11:27:32] 10 ancestry keys
[START] [2021-02-03 11:27:32] build_node_ancestors
[INFO] [2021-02-03 11:27:32] old ancestors deleted.
[STOP] [2021-02-03 11:27:32] build_node_ancestors
[WARN] [2021-02-03 11:27:32] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-02-03 11:27:32] Flattener#flatten
[STOP] [2021-02-03 11:27:32] rebuild_nodes
[START] [2021-02-03 11:27:32] resolve_missing_media_owners
[STOP] [2021-02-03 11:27:32] resolve_missing_media_owners
[START] [2021-02-03 11:27:32] sanitize_media_verbatims
[STOP] [2021-02-03 11:27:32] sanitize_media_verbatims
[START] [2021-02-03 11:27:32] queue_downloads
[STOP] [2021-02-03 11:27:32] queue_downloads
[START] [2021-02-03 11:27:32] parse_names
[WARN] [2021-02-03 11:27:32] I see 10 names which still need to be parsed.
[STOP] [2021-02-03 11:27:33] parse_names
[START] [2021-02-03 11:27:33] denormalize_canonical_names_to_nodes
[STOP] [2021-02-03 11:27:33] denormalize_canonical_names_to_nodes
[START] [2021-02-03 11:27:33] match_nodes
[START] [2021-02-03 11:27:33] map_all_nodes_to_pages
[STOP] [2021-02-03 11:27:33] map_all_nodes_to_pages
[INFO] [2021-02-03 11:27:33] ZERO unmatched nodes (of 10)! Nicely done.
[START] [2021-02-03 11:27:33] update_nodes
[STOP] [2021-02-03 11:27:33] update_nodes
[STOP] [2021-02-03 11:27:33] match_nodes
[START] [2021-02-03 11:27:33] reindex_search
[STOP] [2021-02-03 11:27:33] reindex_search
[START] [2021-02-03 11:27:33] normalize_units
[STOP] [2021-02-03 11:27:33] normalize_units
[START] [2021-02-03 11:27:33] calculate_statistics
[2021-02-03 11:27:33] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-02-03 11:27:33] calculate_statistics
[START] [2021-02-03 11:27:33] complete_harvest_instance
[START] [2021-02-03 11:27:33] overall_tsv_creation
[INFO] [2021-02-03 11:27:33] Processing group of 10 in 1 batches of 10000
[INFO] [2021-02-03 11:28:13] 10 Traits (unfiltered)...
[INFO] [2021-02-03 11:28:49] 10 Traits (filtered)...
[INFO] [2021-02-03 11:28:49] 0 Associations (filtered)...
[INFO] [2021-02-03 11:28:49] 50 metadata added.
[INFO] [2021-02-03 11:28:49] 0 metadata added.
[INFO] [2021-02-03 11:29:21] Average Time: 81.21
[INFO] [2021-02-03 11:29:21] Total Time: 1m48s
[STOP] [2021-02-03 11:29:21] overall_tsv_creation
[INFO] [2021-02-03 11:29:21] Done. Check your files:
[INFO] [2021-02-03 11:29:21] (10 lines) /app/public/data/lewis_taylor_lew/publish_nodes.tsv
[INFO] [2021-02-03 11:29:21] (10 lines) /app/public/data/lewis_taylor_lew/publish_scientific_names.tsv
[INFO] [2021-02-03 11:29:21] (11 lines) /app/public/data/lewis_taylor_lew/publish_traits.tsv
[INFO] [2021-02-03 11:29:21] (51 lines) /app/public/data/lewis_taylor_lew/publish_metadata.tsv
[STOP] [2021-02-03 11:29:21] complete_harvest_instance
[START] [2021-02-03 11:29:21] completed
[STOP] [2021-02-03 11:29:21] completed
[STOP] [2021-02-03 11:29:21] logged process, took 117.08
[INFO] [2021-04-01 13:37:21] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-01 13:37:24] ## remove_type: ScientificName
[INFO] [2021-04-01 13:37:24] ++ Calling delete_all on 10 instances...
[INFO] [2021-04-01 13:37:24] [13:37:24.224] Removed 10 Scientificnames
[INFO] [2021-04-01 13:37:24] ## remove_type: Vernacular
[INFO] [2021-04-01 13:37:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-01 13:37:24] [13:37:24.226] Removed 0 Vernaculars
[INFO] [2021-04-01 13:37:24] ## remove_type: Article
[INFO] [2021-04-01 13:37:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-01 13:37:24] [13:37:24.227] Removed 0 Articles
[INFO] [2021-04-01 13:37:24] ## remove_type: Medium
[INFO] [2021-04-01 13:37:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-01 13:37:24] [13:37:24.229] Removed 0 Media
[INFO] [2021-04-01 13:37:24] ## remove_type: Trait
[INFO] [2021-04-01 13:37:24] ++ Calling delete_all on 40 instances...
[INFO] [2021-04-01 13:37:24] [13:37:24.300] Removed 40 Traits
[INFO] [2021-04-01 13:37:24] ## remove_type: MetaTrait
[INFO] [2021-04-01 13:37:24] ++ Calling delete_all on 20 instances...
[INFO] [2021-04-01 13:37:24] [13:37:24.412] Removed 20 Metatraits
[INFO] [2021-04-01 13:37:24] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-01 13:37:24] ++ Calling delete_all on 10 instances...
[INFO] [2021-04-01 13:37:24] [13:37:24.424] Removed 10 Occurrencemetadata
[INFO] [2021-04-01 13:37:24] ## remove_type: Assoc
[INFO] [2021-04-01 13:37:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-01 13:37:24] [13:37:24.425] Removed 0 Assocs
[INFO] [2021-04-01 13:37:24] ## remove_type: MetaAssoc
[INFO] [2021-04-01 13:37:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-01 13:37:24] [13:37:24.427] Removed 0 Metaassocs
[INFO] [2021-04-01 13:37:24] ## remove_type: Identifier
[INFO] [2021-04-01 13:37:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-01 13:37:24] [13:37:24.432] Removed 0 Identifiers
[INFO] [2021-04-01 13:37:24] ## remove_type: Reference
[INFO] [2021-04-01 13:37:24] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-01 13:37:24] [13:37:24.433] Removed 0 References
[INFO] [2021-04-01 13:37:24] Starting batch with ID 87728857...
[INFO] [2021-04-01 13:37:25] Starting batch with ID 87728857...
[INFO] [2021-04-01 13:37:25] Starting batch with ID 87728857...
[INFO] [2021-04-01 13:37:25] Starting batch with ID 87728857...
[INFO] [2021-04-01 13:37:25] Starting batch with ID 87728857...
[INFO] [2021-04-01 13:37:25] Starting batch with ID 87728857...
[INFO] [2021-04-01 13:37:25] Starting batch with ID 87728857...
[INFO] [2021-04-01 13:37:25] Starting batch with ID 87728857...
[INFO] [2021-04-01 13:37:25] Starting batch with ID 87728857...
[INFO] [2021-04-01 13:37:25] Starting batch with ID 87728857...
[INFO] [2021-04-01 13:37:25] ## remove_type: Node
[INFO] [2021-04-01 13:37:25] ++ Calling delete_all on 10 instances...
[INFO] [2021-04-01 13:37:25] [13:37:25.119] Removed 10 Nodes
[START] [2021-04-01 13:37:25] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-01 13:37:25] Creating resource from OpenData
[START] [2021-04-01 13:37:25] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-01 13:37:25] Parse meta.xml file and create formats with fields
[STOP] [2021-04-01 13:37:27] Parse meta.xml file and create formats with fields
[STOP] [2021-04-01 13:37:27] Creating resource from OpenData
[START] [2021-04-01 13:37:27] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-01 13:37:27] create_harvest_instance
[INFO] [2021-04-01 13:37:27] Created harvest instance #3569
[STOP] [2021-04-01 13:37:27] create_harvest_instance
[START] [2021-04-01 13:37:27] fetch_files
[STOP] [2021-04-01 13:37:27] fetch_files
[START] [2021-04-01 13:37:27] validate_each_file
[INFO] [2021-04-01 13:37:27] Looping over 3 formats...
[INFO] [2021-04-01 13:37:27] ...nodes (/app/public/data/lewis_taylor_lew/taxa.txt)
[INFO] [2021-04-01 13:37:27] Valid: /app/public/converted_csv/lewis_taylor_lew_nodes_3569.csv (10 lines)
[INFO] [2021-04-01 13:37:27] ...occurrences (/app/public/data/lewis_taylor_lew/occurrences.txt)
[INFO] [2021-04-01 13:37:27] Valid: /app/public/converted_csv/lewis_taylor_lew_occurrences_3569.csv (10 lines)
[INFO] [2021-04-01 13:37:27] ...measurements (/app/public/data/lewis_taylor_lew/measurementsorfacts.txt)
[INFO] [2021-04-01 13:37:27] Valid: /app/public/converted_csv/lewis_taylor_lew_measurements_3569.csv (39 lines)
[STOP] [2021-04-01 13:37:27] validate_each_file
[START] [2021-04-01 13:37:27] convert_to_csv
[INFO] [2021-04-01 13:37:27] Looping over 3 formats...
[INFO] [2021-04-01 13:37:27] ...nodes (/app/public/data/lewis_taylor_lew/taxa.txt)
[CMD] [2021-04-01 13:37:27] /usr/bin/sort /app/public/converted_csv/lewis_taylor_lew_nodes_3569.csv > /app/public/converted_csv/lewis_taylor_lew_nodes_3569.csv_sorted
[INFO] [2021-04-01 13:37:27] Converted: /app/public/converted_csv/lewis_taylor_lew_nodes_3569.csv (10 lines)
[INFO] [2021-04-01 13:37:27] ...occurrences (/app/public/data/lewis_taylor_lew/occurrences.txt)
[CMD] [2021-04-01 13:37:27] /usr/bin/sort /app/public/converted_csv/lewis_taylor_lew_occurrences_3569.csv > /app/public/converted_csv/lewis_taylor_lew_occurrences_3569.csv_sorted
[INFO] [2021-04-01 13:37:28] Converted: /app/public/converted_csv/lewis_taylor_lew_occurrences_3569.csv (10 lines)
[INFO] [2021-04-01 13:37:28] ...measurements (/app/public/data/lewis_taylor_lew/measurementsorfacts.txt)
[CMD] [2021-04-01 13:37:28] /usr/bin/sort /app/public/converted_csv/lewis_taylor_lew_measurements_3569.csv > /app/public/converted_csv/lewis_taylor_lew_measurements_3569.csv_sorted
[INFO] [2021-04-01 13:37:28] Converted: /app/public/converted_csv/lewis_taylor_lew_measurements_3569.csv (39 lines)
[STOP] [2021-04-01 13:37:28] convert_to_csv
[START] [2021-04-01 13:37:28] calculate_delta
[INFO] [2021-04-01 13:37:28] Looping over 3 formats...
[INFO] [2021-04-01 13:37:28] ...nodes (/app/public/data/lewis_taylor_lew/taxa.txt)
[CMD] [2021-04-01 13:37:28] echo "0a" > /app/public/diff/lewis_taylor_lew_nodes_3569.diff
[CMD] [2021-04-01 13:37:28] tail -n +1 /app/public/converted_csv/lewis_taylor_lew_nodes_3569.csv >> /app/public/diff/lewis_taylor_lew_nodes_3569.diff
[CMD] [2021-04-01 13:37:28] echo "." >> /app/public/diff/lewis_taylor_lew_nodes_3569.diff
[INFO] [2021-04-01 13:37:28] Created diff: /app/public/diff/lewis_taylor_lew_nodes_3569.diff (12 lines)
[INFO] [2021-04-01 13:37:28] ...occurrences (/app/public/data/lewis_taylor_lew/occurrences.txt)
[CMD] [2021-04-01 13:37:28] echo "0a" > /app/public/diff/lewis_taylor_lew_occurrences_3569.diff
[CMD] [2021-04-01 13:37:28] tail -n +1 /app/public/converted_csv/lewis_taylor_lew_occurrences_3569.csv >> /app/public/diff/lewis_taylor_lew_occurrences_3569.diff
[CMD] [2021-04-01 13:37:28] echo "." >> /app/public/diff/lewis_taylor_lew_occurrences_3569.diff
[INFO] [2021-04-01 13:37:29] Created diff: /app/public/diff/lewis_taylor_lew_occurrences_3569.diff (12 lines)
[INFO] [2021-04-01 13:37:29] ...measurements (/app/public/data/lewis_taylor_lew/measurementsorfacts.txt)
[CMD] [2021-04-01 13:37:29] echo "0a" > /app/public/diff/lewis_taylor_lew_measurements_3569.diff
[CMD] [2021-04-01 13:37:29] tail -n +1 /app/public/converted_csv/lewis_taylor_lew_measurements_3569.csv >> /app/public/diff/lewis_taylor_lew_measurements_3569.diff
[CMD] [2021-04-01 13:37:29] echo "." >> /app/public/diff/lewis_taylor_lew_measurements_3569.diff
[INFO] [2021-04-01 13:37:29] Created diff: /app/public/diff/lewis_taylor_lew_measurements_3569.diff (41 lines)
[STOP] [2021-04-01 13:37:29] calculate_delta
[START] [2021-04-01 13:37:29] parse_diff_and_store
[INFO] [2021-04-01 13:37:29] Handling diff: /app/public/diff/lewis_taylor_lew_nodes_3569.diff (12 lines)
[INFO] [2021-04-01 13:37:29] Loading nodes diff file into memory (12 /app/public/diff/lewis_taylor_lew_nodes_3569.diff lines)...
[INFO] [2021-04-01 13:37:29] Handling diff: /app/public/diff/lewis_taylor_lew_occurrences_3569.diff (12 lines)
[INFO] [2021-04-01 13:37:29] Loading occurrences diff file into memory (12 /app/public/diff/lewis_taylor_lew_occurrences_3569.diff lines)...
[INFO] [2021-04-01 13:37:30] Handling diff: /app/public/diff/lewis_taylor_lew_measurements_3569.diff (41 lines)
[INFO] [2021-04-01 13:37:30] Loading measurements diff file into memory (41 /app/public/diff/lewis_taylor_lew_measurements_3569.diff lines)...
[INFO] [2021-04-01 13:37:30] Storing 10 ScientificNames
[INFO] [2021-04-01 13:37:30] Processing group of 10 in 1 groups of 1000
[INFO] [2021-04-01 13:37:30] Average Time: 0.0
[INFO] [2021-04-01 13:37:30] Total Time: 1s
[INFO] [2021-04-01 13:37:30] Storing 10 Nodes
[INFO] [2021-04-01 13:37:30] Processing group of 10 in 1 groups of 1000
[INFO] [2021-04-01 13:37:30] Average Time: 0.0
[INFO] [2021-04-01 13:37:30] Total Time: 1s
[INFO] [2021-04-01 13:37:30] Storing 10 Occurrences
[INFO] [2021-04-01 13:37:30] Processing group of 10 in 1 groups of 1000
[INFO] [2021-04-01 13:37:30] Average Time: 0.0
[INFO] [2021-04-01 13:37:30] Total Time: 1s
[INFO] [2021-04-01 13:37:30] Storing 10 OccurrenceMetadata
[INFO] [2021-04-01 13:37:30] Processing group of 10 in 1 groups of 1000
[INFO] [2021-04-01 13:37:30] Average Time: 0.01
[INFO] [2021-04-01 13:37:30] Total Time: 1s
[INFO] [2021-04-01 13:37:30] Storing 39 Traits
[INFO] [2021-04-01 13:37:30] Processing group of 39 in 1 groups of 1000
[INFO] [2021-04-01 13:37:30] Average Time: 0.01
[INFO] [2021-04-01 13:37:30] Total Time: 1s
[INFO] [2021-04-01 13:37:30] Storing 20 MetaTraits
[INFO] [2021-04-01 13:37:30] Processing group of 20 in 1 groups of 1000
[INFO] [2021-04-01 13:37:30] Average Time: 0.0
[INFO] [2021-04-01 13:37:30] Total Time: 1s
[STOP] [2021-04-01 13:37:30] parse_diff_and_store
[START] [2021-04-01 13:37:30] resolve_keys
[INFO] [2021-04-01 13:37:36] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-01 13:37:36] traits to occurrences...
[INFO] [2021-04-01 13:37:36] traits to nodes (through occurrences)...
[INFO] [2021-04-01 13:37:36] Traits to sex term...
[INFO] [2021-04-01 13:37:36] Traits to lifestage term...
[INFO] [2021-04-01 13:37:36] MetaTraits to traits...
[INFO] [2021-04-01 13:37:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-01 13:37:36] Assocs to occurrences...
[INFO] [2021-04-01 13:37:36] Assocs to nodes...
[INFO] [2021-04-01 13:37:36] Assoc to sex term...
[INFO] [2021-04-01 13:37:36] Assoc to lifestage term...
[INFO] [2021-04-01 13:37:36] MetaAssoc to assocs...
[STOP] [2021-04-01 13:37:36] resolve_keys
[START] [2021-04-01 13:37:36] hold_for_later_1
[STOP] [2021-04-01 13:37:36] hold_for_later_1
[START] [2021-04-01 13:37:36] hold_for_later_2
[STOP] [2021-04-01 13:37:36] hold_for_later_2
[START] [2021-04-01 13:37:36] resolve_missing_parents
[STOP] [2021-04-01 13:37:36] resolve_missing_parents
[START] [2021-04-01 13:37:36] rebuild_nodes
[START] [2021-04-01 13:37:36] Flattener#flatten
[START] [2021-04-01 13:37:36] Flattener#study_resource
[START] [2021-04-01 13:37:36] Flattener#build_ancestry
[STOP] [2021-04-01 13:37:36] Flattener#build_ancestry
[INFO] [2021-04-01 13:37:36] 10 ancestry keys
[START] [2021-04-01 13:37:36] build_node_ancestors
[INFO] [2021-04-01 13:37:36] old ancestors deleted.
[STOP] [2021-04-01 13:37:36] build_node_ancestors
[WARN] [2021-04-01 13:37:36] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-01 13:37:36] Flattener#flatten
[STOP] [2021-04-01 13:37:36] rebuild_nodes
[START] [2021-04-01 13:37:36] resolve_missing_media_owners
[STOP] [2021-04-01 13:37:36] resolve_missing_media_owners
[START] [2021-04-01 13:37:36] sanitize_media_verbatims
[STOP] [2021-04-01 13:37:36] sanitize_media_verbatims
[START] [2021-04-01 13:37:36] queue_downloads
[STOP] [2021-04-01 13:37:36] queue_downloads
[START] [2021-04-01 13:37:36] parse_names
[WARN] [2021-04-01 13:37:36] I see 10 names which still need to be parsed.
[STOP] [2021-04-01 13:37:37] parse_names
[START] [2021-04-01 13:37:37] denormalize_canonical_names_to_nodes
[STOP] [2021-04-01 13:37:37] denormalize_canonical_names_to_nodes
[START] [2021-04-01 13:37:37] match_nodes
[START] [2021-04-01 13:37:37] map_all_nodes_to_pages
[STOP] [2021-04-01 13:37:37] map_all_nodes_to_pages
[INFO] [2021-04-01 13:37:37] ZERO unmatched nodes (of 10)! Nicely done.
[START] [2021-04-01 13:37:37] update_nodes
[STOP] [2021-04-01 13:37:37] update_nodes
[STOP] [2021-04-01 13:37:37] match_nodes
[START] [2021-04-01 13:37:37] reindex_search
[STOP] [2021-04-01 13:37:37] reindex_search
[START] [2021-04-01 13:37:37] normalize_units
[STOP] [2021-04-01 13:37:37] normalize_units
[START] [2021-04-01 13:37:37] calculate_statistics
[2021-04-01 13:37:37] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-01 13:37:37] calculate_statistics
[START] [2021-04-01 13:37:37] complete_harvest_instance
[START] [2021-04-01 13:37:37] overall_tsv_creation
[INFO] [2021-04-01 13:37:37] Processing group of 10 in 1 batches of 10000
[INFO] [2021-04-01 13:38:14] 10 Traits (unfiltered)...
[INFO] [2021-04-01 13:38:48] 10 Traits (filtered)...
[INFO] [2021-04-01 13:38:48] 0 Associations (filtered)...
[INFO] [2021-04-01 13:38:48] 29 metadata added.
[INFO] [2021-04-01 13:38:48] 0 metadata added.
[INFO] [2021-04-01 13:39:17] Average Time: 74.36
[INFO] [2021-04-01 13:39:17] Total Time: 1m40s
[STOP] [2021-04-01 13:39:17] overall_tsv_creation
[INFO] [2021-04-01 13:39:17] Done. Check your files:
[INFO] [2021-04-01 13:39:17] (10 lines) /app/public/data/lewis_taylor_lew/publish_nodes.tsv
[INFO] [2021-04-01 13:39:17] (10 lines) /app/public/data/lewis_taylor_lew/publish_scientific_names.tsv
[INFO] [2021-04-01 13:39:17] (11 lines) /app/public/data/lewis_taylor_lew/publish_traits.tsv
[INFO] [2021-04-01 13:39:18] (30 lines) /app/public/data/lewis_taylor_lew/publish_metadata.tsv
[STOP] [2021-04-01 13:39:18] complete_harvest_instance
[START] [2021-04-01 13:39:18] completed
[STOP] [2021-04-01 13:39:18] completed
[STOP] [2021-04-01 13:39:18] logged process, took 110.65
Latest Process