Harvest for Insect Development Created 29 Apr 15:43

Stage: completed
Fetched: 29 Apr 15:43
Validated: 29 Apr 15:43
Deltas Created 29 Apr 15:43
Units Normalized: 29 Apr 15:44
Ancestry Built: 29 Apr 15:44
Nodes Matched: 29 Apr 15:44
Names Parsed: 29 Apr 15:44
New Models Stored: 29 Apr 15:43
Indexed: 29 Apr 15:44
Completed: 29 Apr 15:46
Time to Harvest: less than a minute
Harvesting Log

(485 lines)
# Logfile created on 2021-04-29 14:02:44 -0400 by logger.rb/66358
[START] [2021-04-29 14:02:45] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 14:02:45] Creating resource from OpenData
[START] [2021-04-29 14:02:45] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 14:02:45] Parse meta.xml file and create formats with fields
[STOP] [2021-04-29 14:02:45] Parse meta.xml file and create formats with fields
[STOP] [2021-04-29 14:02:45] Creating resource from OpenData
[INFO] [2021-04-29 14:03:08] ## HARVEST: type = -harvest
[START] [2021-04-29 14:03:13] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 14:03:13] create_harvest_instance
[INFO] [2021-04-29 14:03:13] Created harvest instance #3836
[STOP] [2021-04-29 14:03:13] create_harvest_instance
[START] [2021-04-29 14:03:13] fetch_files
[STOP] [2021-04-29 14:03:13] fetch_files
[START] [2021-04-29 14:03:13] validate_each_file
[INFO] [2021-04-29 14:03:13] Looping over 3 formats...
[INFO] [2021-04-29 14:03:13] ...nodes (/app/public/data/insect_developme/taxa.txt)
[INFO] [2021-04-29 14:03:13] Valid: /app/public/converted_csv/insect_developme_nodes_3836.csv (11 lines)
[INFO] [2021-04-29 14:03:13] ...occurrences (/app/public/data/insect_developme/occurrences.txt)
[INFO] [2021-04-29 14:03:13] Valid: /app/public/converted_csv/insect_developme_occurrences_3836.csv (11 lines)
[INFO] [2021-04-29 14:03:13] ...measurements (/app/public/data/insect_developme/measurementsorfacts.txt)
[INFO] [2021-04-29 14:03:13] Valid: /app/public/converted_csv/insect_developme_measurements_3836.csv (22 lines)
[STOP] [2021-04-29 14:03:13] validate_each_file
[START] [2021-04-29 14:03:13] convert_to_csv
[INFO] [2021-04-29 14:03:13] Looping over 3 formats...
[INFO] [2021-04-29 14:03:13] ...nodes (/app/public/data/insect_developme/taxa.txt)
[CMD] [2021-04-29 14:03:13] /usr/bin/sort /app/public/converted_csv/insect_developme_nodes_3836.csv > /app/public/converted_csv/insect_developme_nodes_3836.csv_sorted
[INFO] [2021-04-29 14:03:13] Converted: /app/public/converted_csv/insect_developme_nodes_3836.csv (11 lines)
[INFO] [2021-04-29 14:03:13] ...occurrences (/app/public/data/insect_developme/occurrences.txt)
[CMD] [2021-04-29 14:03:13] /usr/bin/sort /app/public/converted_csv/insect_developme_occurrences_3836.csv > /app/public/converted_csv/insect_developme_occurrences_3836.csv_sorted
[INFO] [2021-04-29 14:03:13] Converted: /app/public/converted_csv/insect_developme_occurrences_3836.csv (11 lines)
[INFO] [2021-04-29 14:03:13] ...measurements (/app/public/data/insect_developme/measurementsorfacts.txt)
[CMD] [2021-04-29 14:03:13] /usr/bin/sort /app/public/converted_csv/insect_developme_measurements_3836.csv > /app/public/converted_csv/insect_developme_measurements_3836.csv_sorted
[INFO] [2021-04-29 14:03:13] Converted: /app/public/converted_csv/insect_developme_measurements_3836.csv (22 lines)
[STOP] [2021-04-29 14:03:13] convert_to_csv
[START] [2021-04-29 14:03:13] calculate_delta
[INFO] [2021-04-29 14:03:13] Looping over 3 formats...
[INFO] [2021-04-29 14:03:13] ...nodes (/app/public/data/insect_developme/taxa.txt)
[CMD] [2021-04-29 14:03:13] echo "0a" > /app/public/diff/insect_developme_nodes_3836.diff
[CMD] [2021-04-29 14:03:13] tail -n +1 /app/public/converted_csv/insect_developme_nodes_3836.csv >> /app/public/diff/insect_developme_nodes_3836.diff
[CMD] [2021-04-29 14:03:13] echo "." >> /app/public/diff/insect_developme_nodes_3836.diff
[INFO] [2021-04-29 14:03:13] Created diff: /app/public/diff/insect_developme_nodes_3836.diff (13 lines)
[INFO] [2021-04-29 14:03:13] ...occurrences (/app/public/data/insect_developme/occurrences.txt)
[CMD] [2021-04-29 14:03:13] echo "0a" > /app/public/diff/insect_developme_occurrences_3836.diff
[CMD] [2021-04-29 14:03:13] tail -n +1 /app/public/converted_csv/insect_developme_occurrences_3836.csv >> /app/public/diff/insect_developme_occurrences_3836.diff
[CMD] [2021-04-29 14:03:13] echo "." >> /app/public/diff/insect_developme_occurrences_3836.diff
[INFO] [2021-04-29 14:03:13] Created diff: /app/public/diff/insect_developme_occurrences_3836.diff (13 lines)
[INFO] [2021-04-29 14:03:13] ...measurements (/app/public/data/insect_developme/measurementsorfacts.txt)
[CMD] [2021-04-29 14:03:13] echo "0a" > /app/public/diff/insect_developme_measurements_3836.diff
[CMD] [2021-04-29 14:03:13] tail -n +1 /app/public/converted_csv/insect_developme_measurements_3836.csv >> /app/public/diff/insect_developme_measurements_3836.diff
[CMD] [2021-04-29 14:03:13] echo "." >> /app/public/diff/insect_developme_measurements_3836.diff
[INFO] [2021-04-29 14:03:13] Created diff: /app/public/diff/insect_developme_measurements_3836.diff (24 lines)
[STOP] [2021-04-29 14:03:13] calculate_delta
[START] [2021-04-29 14:03:13] parse_diff_and_store
[INFO] [2021-04-29 14:03:13] Handling diff: /app/public/diff/insect_developme_nodes_3836.diff (13 lines)
[INFO] [2021-04-29 14:03:13] Loading nodes diff file into memory (13 /app/public/diff/insect_developme_nodes_3836.diff lines)...
[INFO] [2021-04-29 14:03:13] Handling diff: /app/public/diff/insect_developme_occurrences_3836.diff (13 lines)
[INFO] [2021-04-29 14:03:13] Loading occurrences diff file into memory (13 /app/public/diff/insect_developme_occurrences_3836.diff lines)...
[INFO] [2021-04-29 14:03:15] Handling diff: /app/public/diff/insect_developme_measurements_3836.diff (24 lines)
[INFO] [2021-04-29 14:03:15] Loading measurements diff file into memory (24 /app/public/diff/insect_developme_measurements_3836.diff lines)...
[INFO] [2021-04-29 14:03:15] Storing 11 ScientificNames
[INFO] [2021-04-29 14:03:15] Processing group of 11 in 1 groups of 1000
[INFO] [2021-04-29 14:03:15] Average Time: 0.01
[INFO] [2021-04-29 14:03:15] Total Time: 1s
[INFO] [2021-04-29 14:03:15] Storing 11 Nodes
[INFO] [2021-04-29 14:03:15] Processing group of 11 in 1 groups of 1000
[INFO] [2021-04-29 14:03:15] Average Time: 0.0
[INFO] [2021-04-29 14:03:15] Total Time: 1s
[INFO] [2021-04-29 14:03:15] Storing 11 Occurrences
[INFO] [2021-04-29 14:03:15] Processing group of 11 in 1 groups of 1000
[INFO] [2021-04-29 14:03:15] Average Time: 0.04
[INFO] [2021-04-29 14:03:15] Total Time: 1s
[INFO] [2021-04-29 14:03:15] Storing 1 OccurrenceMetadata
[INFO] [2021-04-29 14:03:15] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-29 14:03:15] Average Time: 0.04
[INFO] [2021-04-29 14:03:15] Total Time: 1s
[INFO] [2021-04-29 14:03:15] Storing 22 Traits
[INFO] [2021-04-29 14:03:15] Processing group of 22 in 1 groups of 1000
[INFO] [2021-04-29 14:03:15] Average Time: 0.1
[INFO] [2021-04-29 14:03:15] Total Time: 1s
[INFO] [2021-04-29 14:03:15] Storing 11 MetaTraits
[INFO] [2021-04-29 14:03:15] Processing group of 11 in 1 groups of 1000
[INFO] [2021-04-29 14:03:15] Average Time: 0.02
[INFO] [2021-04-29 14:03:15] Total Time: 1s
[STOP] [2021-04-29 14:03:15] parse_diff_and_store
[START] [2021-04-29 14:03:15] resolve_keys
[INFO] [2021-04-29 14:03:22] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-29 14:03:22] traits to occurrences...
[INFO] [2021-04-29 14:03:22] traits to nodes (through occurrences)...
[INFO] [2021-04-29 14:03:22] Traits to sex term...
[INFO] [2021-04-29 14:03:22] Traits to lifestage term...
[INFO] [2021-04-29 14:03:22] MetaTraits to traits...
[INFO] [2021-04-29 14:03:22] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-29 14:03:22] Assocs to occurrences...
[INFO] [2021-04-29 14:03:22] Assocs to nodes...
[INFO] [2021-04-29 14:03:22] Assoc to sex term...
[INFO] [2021-04-29 14:03:22] Assoc to lifestage term...
[INFO] [2021-04-29 14:03:22] MetaAssoc to assocs...
[STOP] [2021-04-29 14:03:22] resolve_keys
[START] [2021-04-29 14:03:22] hold_for_later_1
[STOP] [2021-04-29 14:03:22] hold_for_later_1
[START] [2021-04-29 14:03:22] hold_for_later_2
[STOP] [2021-04-29 14:03:22] hold_for_later_2
[START] [2021-04-29 14:03:22] resolve_missing_parents
[STOP] [2021-04-29 14:03:22] resolve_missing_parents
[START] [2021-04-29 14:03:22] rebuild_nodes
[START] [2021-04-29 14:03:22] Flattener#flatten
[START] [2021-04-29 14:03:22] Flattener#study_resource
[START] [2021-04-29 14:03:22] Flattener#build_ancestry
[STOP] [2021-04-29 14:03:22] Flattener#build_ancestry
[INFO] [2021-04-29 14:03:22] 11 ancestry keys
[START] [2021-04-29 14:03:22] build_node_ancestors
[INFO] [2021-04-29 14:03:22] old ancestors deleted.
[STOP] [2021-04-29 14:03:22] build_node_ancestors
[WARN] [2021-04-29 14:03:22] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-29 14:03:22] Flattener#flatten
[STOP] [2021-04-29 14:03:22] rebuild_nodes
[START] [2021-04-29 14:03:22] resolve_missing_media_owners
[STOP] [2021-04-29 14:03:22] resolve_missing_media_owners
[START] [2021-04-29 14:03:22] sanitize_media_verbatims
[STOP] [2021-04-29 14:03:22] sanitize_media_verbatims
[START] [2021-04-29 14:03:22] queue_downloads
[STOP] [2021-04-29 14:03:22] queue_downloads
[START] [2021-04-29 14:03:22] parse_names
[WARN] [2021-04-29 14:03:22] I see 11 names which still need to be parsed.
[STOP] [2021-04-29 14:03:23] parse_names
[START] [2021-04-29 14:03:23] denormalize_canonical_names_to_nodes
[STOP] [2021-04-29 14:03:23] denormalize_canonical_names_to_nodes
[START] [2021-04-29 14:03:23] match_nodes
[START] [2021-04-29 14:03:23] map_all_nodes_to_pages
[STOP] [2021-04-29 14:03:23] map_all_nodes_to_pages
[INFO] [2021-04-29 14:03:23] ZERO unmatched nodes (of 11)! Nicely done.
[START] [2021-04-29 14:03:23] update_nodes
[STOP] [2021-04-29 14:03:23] update_nodes
[STOP] [2021-04-29 14:03:23] match_nodes
[START] [2021-04-29 14:03:23] reindex_search
[STOP] [2021-04-29 14:03:24] reindex_search
[START] [2021-04-29 14:03:24] normalize_units
[STOP] [2021-04-29 14:03:24] normalize_units
[START] [2021-04-29 14:03:24] calculate_statistics
[2021-04-29 14:03:24] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-29 14:03:24] calculate_statistics
[START] [2021-04-29 14:03:24] complete_harvest_instance
[START] [2021-04-29 14:03:24] overall_tsv_creation
[INFO] [2021-04-29 14:03:24] Processing group of 11 in 1 batches of 10000
[INFO] [2021-04-29 14:05:51] 11 Traits (unfiltered)...
[INFO] [2021-04-29 14:06:27] 11 Traits (filtered)...
[INFO] [2021-04-29 14:06:27] 0 Associations (filtered)...
[INFO] [2021-04-29 14:06:27] 11 metadata added.
[INFO] [2021-04-29 14:06:27] 0 metadata added.
[INFO] [2021-04-29 14:06:53] Average Time: 102.27
[INFO] [2021-04-29 14:06:53] Total Time: 3m30s
[STOP] [2021-04-29 14:06:53] overall_tsv_creation
[INFO] [2021-04-29 14:06:53] Done. Check your files:
[INFO] [2021-04-29 14:06:53] (11 lines) /app/public/data/insect_developme/publish_nodes.tsv
[INFO] [2021-04-29 14:06:53] (11 lines) /app/public/data/insect_developme/publish_scientific_names.tsv
[INFO] [2021-04-29 14:06:53] (12 lines) /app/public/data/insect_developme/publish_traits.tsv
[INFO] [2021-04-29 14:06:53] (12 lines) /app/public/data/insect_developme/publish_metadata.tsv
[STOP] [2021-04-29 14:06:53] complete_harvest_instance
[START] [2021-04-29 14:06:53] completed
[STOP] [2021-04-29 14:06:53] completed
[STOP] [2021-04-29 14:06:53] logged process, took 220.26
[INFO] [2021-04-29 15:43:44] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-29 15:43:47] ## remove_type: ScientificName
[INFO] [2021-04-29 15:43:47] ++ Calling delete_all on 11 instances...
[INFO] [2021-04-29 15:43:47] [15:43:47.012] Removed 11 Scientificnames
[INFO] [2021-04-29 15:43:47] ## remove_type: Vernacular
[INFO] [2021-04-29 15:43:47] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 15:43:47] [15:43:47.014] Removed 0 Vernaculars
[INFO] [2021-04-29 15:43:47] ## remove_type: Article
[INFO] [2021-04-29 15:43:47] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 15:43:47] [15:43:47.015] Removed 0 Articles
[INFO] [2021-04-29 15:43:47] ## remove_type: Medium
[INFO] [2021-04-29 15:43:47] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 15:43:47] [15:43:47.017] Removed 0 Media
[INFO] [2021-04-29 15:43:47] ## remove_type: Trait
[INFO] [2021-04-29 15:43:47] ++ Calling delete_all on 22 instances...
[INFO] [2021-04-29 15:43:47] [15:43:47.028] Removed 22 Traits
[INFO] [2021-04-29 15:43:47] ## remove_type: MetaTrait
[INFO] [2021-04-29 15:43:47] ++ Calling delete_all on 11 instances...
[INFO] [2021-04-29 15:43:47] [15:43:47.029] Removed 11 Metatraits
[INFO] [2021-04-29 15:43:47] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-29 15:43:47] ++ Calling delete_all on 1 instances...
[INFO] [2021-04-29 15:43:47] [15:43:47.036] Removed 1 Occurrencemetadata
[INFO] [2021-04-29 15:43:47] ## remove_type: Assoc
[INFO] [2021-04-29 15:43:47] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 15:43:47] [15:43:47.037] Removed 0 Assocs
[INFO] [2021-04-29 15:43:47] ## remove_type: MetaAssoc
[INFO] [2021-04-29 15:43:47] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 15:43:47] [15:43:47.039] Removed 0 Metaassocs
[INFO] [2021-04-29 15:43:47] ## remove_type: Identifier
[INFO] [2021-04-29 15:43:47] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 15:43:47] [15:43:47.040] Removed 0 Identifiers
[INFO] [2021-04-29 15:43:47] ## remove_type: Reference
[INFO] [2021-04-29 15:43:47] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-29 15:43:47] [15:43:47.065] Removed 0 References
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:47] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:48] Starting batch with ID 93345451...
[INFO] [2021-04-29 15:43:48] Starting batch with ID 93345459...
[INFO] [2021-04-29 15:43:49] Starting batch with ID 93345459...
[INFO] [2021-04-29 15:43:49] Starting batch with ID 93345457...
[INFO] [2021-04-29 15:43:49] Starting batch with ID 93345457...
[INFO] [2021-04-29 15:43:49] Starting batch with ID 93345457...
[INFO] [2021-04-29 15:43:49] Starting batch with ID 93345457...
[INFO] [2021-04-29 15:43:50] Starting batch with ID 93345454...
[INFO] [2021-04-29 15:43:50] Starting batch with ID 93345450...
[INFO] [2021-04-29 15:43:50] Starting batch with ID 93345450...
[INFO] [2021-04-29 15:43:51] ## remove_type: Node
[INFO] [2021-04-29 15:43:51] ++ Calling delete_all on 11 instances...
[INFO] [2021-04-29 15:43:51] [15:43:51.200] Removed 11 Nodes
[START] [2021-04-29 15:43:51] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 15:43:51] Creating resource from OpenData
[START] [2021-04-29 15:43:51] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 15:43:51] Parse meta.xml file and create formats with fields
[STOP] [2021-04-29 15:43:51] Parse meta.xml file and create formats with fields
[STOP] [2021-04-29 15:43:51] Creating resource from OpenData
[START] [2021-04-29 15:43:51] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-29 15:43:51] create_harvest_instance
[INFO] [2021-04-29 15:43:51] Created harvest instance #3838
[STOP] [2021-04-29 15:43:51] create_harvest_instance
[START] [2021-04-29 15:43:51] fetch_files
[STOP] [2021-04-29 15:43:51] fetch_files
[START] [2021-04-29 15:43:51] validate_each_file
[INFO] [2021-04-29 15:43:51] Looping over 3 formats...
[INFO] [2021-04-29 15:43:51] ...nodes (/app/public/data/insect_developme/taxa.txt)
[INFO] [2021-04-29 15:43:51] Valid: /app/public/converted_csv/insect_developme_nodes_3838.csv (14 lines)
[INFO] [2021-04-29 15:43:51] ...occurrences (/app/public/data/insect_developme/occurrences.txt)
[INFO] [2021-04-29 15:43:51] Valid: /app/public/converted_csv/insect_developme_occurrences_3838.csv (14 lines)
[INFO] [2021-04-29 15:43:51] ...measurements (/app/public/data/insect_developme/measurementsorfacts.txt)
[INFO] [2021-04-29 15:43:51] Valid: /app/public/converted_csv/insect_developme_measurements_3838.csv (26 lines)
[STOP] [2021-04-29 15:43:51] validate_each_file
[START] [2021-04-29 15:43:51] convert_to_csv
[INFO] [2021-04-29 15:43:51] Looping over 3 formats...
[INFO] [2021-04-29 15:43:51] ...nodes (/app/public/data/insect_developme/taxa.txt)
[CMD] [2021-04-29 15:43:51] /usr/bin/sort /app/public/converted_csv/insect_developme_nodes_3838.csv > /app/public/converted_csv/insect_developme_nodes_3838.csv_sorted
[INFO] [2021-04-29 15:43:51] Converted: /app/public/converted_csv/insect_developme_nodes_3838.csv (14 lines)
[INFO] [2021-04-29 15:43:51] ...occurrences (/app/public/data/insect_developme/occurrences.txt)
[CMD] [2021-04-29 15:43:51] /usr/bin/sort /app/public/converted_csv/insect_developme_occurrences_3838.csv > /app/public/converted_csv/insect_developme_occurrences_3838.csv_sorted
[INFO] [2021-04-29 15:43:51] Converted: /app/public/converted_csv/insect_developme_occurrences_3838.csv (14 lines)
[INFO] [2021-04-29 15:43:51] ...measurements (/app/public/data/insect_developme/measurementsorfacts.txt)
[CMD] [2021-04-29 15:43:51] /usr/bin/sort /app/public/converted_csv/insect_developme_measurements_3838.csv > /app/public/converted_csv/insect_developme_measurements_3838.csv_sorted
[INFO] [2021-04-29 15:43:51] Converted: /app/public/converted_csv/insect_developme_measurements_3838.csv (26 lines)
[STOP] [2021-04-29 15:43:51] convert_to_csv
[START] [2021-04-29 15:43:51] calculate_delta
[INFO] [2021-04-29 15:43:51] Looping over 3 formats...
[INFO] [2021-04-29 15:43:51] ...nodes (/app/public/data/insect_developme/taxa.txt)
[CMD] [2021-04-29 15:43:51] echo "0a" > /app/public/diff/insect_developme_nodes_3838.diff
[CMD] [2021-04-29 15:43:51] tail -n +1 /app/public/converted_csv/insect_developme_nodes_3838.csv >> /app/public/diff/insect_developme_nodes_3838.diff
[CMD] [2021-04-29 15:43:51] echo "." >> /app/public/diff/insect_developme_nodes_3838.diff
[INFO] [2021-04-29 15:43:51] Created diff: /app/public/diff/insect_developme_nodes_3838.diff (16 lines)
[INFO] [2021-04-29 15:43:51] ...occurrences (/app/public/data/insect_developme/occurrences.txt)
[CMD] [2021-04-29 15:43:51] echo "0a" > /app/public/diff/insect_developme_occurrences_3838.diff
[CMD] [2021-04-29 15:43:51] tail -n +1 /app/public/converted_csv/insect_developme_occurrences_3838.csv >> /app/public/diff/insect_developme_occurrences_3838.diff
[CMD] [2021-04-29 15:43:51] echo "." >> /app/public/diff/insect_developme_occurrences_3838.diff
[INFO] [2021-04-29 15:43:51] Created diff: /app/public/diff/insect_developme_occurrences_3838.diff (16 lines)
[INFO] [2021-04-29 15:43:51] ...measurements (/app/public/data/insect_developme/measurementsorfacts.txt)
[CMD] [2021-04-29 15:43:51] echo "0a" > /app/public/diff/insect_developme_measurements_3838.diff
[CMD] [2021-04-29 15:43:51] tail -n +1 /app/public/converted_csv/insect_developme_measurements_3838.csv >> /app/public/diff/insect_developme_measurements_3838.diff
[CMD] [2021-04-29 15:43:51] echo "." >> /app/public/diff/insect_developme_measurements_3838.diff
[INFO] [2021-04-29 15:43:51] Created diff: /app/public/diff/insect_developme_measurements_3838.diff (28 lines)
[STOP] [2021-04-29 15:43:51] calculate_delta
[START] [2021-04-29 15:43:51] parse_diff_and_store
[INFO] [2021-04-29 15:43:51] Handling diff: /app/public/diff/insect_developme_nodes_3838.diff (16 lines)
[INFO] [2021-04-29 15:43:51] Loading nodes diff file into memory (16 /app/public/diff/insect_developme_nodes_3838.diff lines)...
[INFO] [2021-04-29 15:43:51] Handling diff: /app/public/diff/insect_developme_occurrences_3838.diff (16 lines)
[INFO] [2021-04-29 15:43:51] Loading occurrences diff file into memory (16 /app/public/diff/insect_developme_occurrences_3838.diff lines)...
[INFO] [2021-04-29 15:43:51] Handling diff: /app/public/diff/insect_developme_measurements_3838.diff (28 lines)
[INFO] [2021-04-29 15:43:51] Loading measurements diff file into memory (28 /app/public/diff/insect_developme_measurements_3838.diff lines)...
[INFO] [2021-04-29 15:43:51] Storing 14 ScientificNames
[INFO] [2021-04-29 15:43:51] Processing group of 14 in 1 groups of 1000
[INFO] [2021-04-29 15:43:51] Average Time: 0.01
[INFO] [2021-04-29 15:43:51] Total Time: 1s
[INFO] [2021-04-29 15:43:51] Storing 14 Nodes
[INFO] [2021-04-29 15:43:51] Processing group of 14 in 1 groups of 1000
[INFO] [2021-04-29 15:43:52] Average Time: 0.02
[INFO] [2021-04-29 15:43:52] Total Time: 1s
[INFO] [2021-04-29 15:43:52] Storing 14 Occurrences
[INFO] [2021-04-29 15:43:52] Processing group of 14 in 1 groups of 1000
[INFO] [2021-04-29 15:43:52] Average Time: 0.01
[INFO] [2021-04-29 15:43:52] Total Time: 1s
[INFO] [2021-04-29 15:43:52] Storing 1 OccurrenceMetadata
[INFO] [2021-04-29 15:43:52] Processing group of 1 in 1 groups of 1000
[INFO] [2021-04-29 15:43:52] Average Time: 0.0
[INFO] [2021-04-29 15:43:52] Total Time: 1s
[INFO] [2021-04-29 15:43:52] Storing 26 Traits
[INFO] [2021-04-29 15:43:52] Processing group of 26 in 1 groups of 1000
[INFO] [2021-04-29 15:43:52] Average Time: 0.04
[INFO] [2021-04-29 15:43:52] Total Time: 1s
[INFO] [2021-04-29 15:43:52] Storing 13 MetaTraits
[INFO] [2021-04-29 15:43:52] Processing group of 13 in 1 groups of 1000
[INFO] [2021-04-29 15:43:52] Average Time: 0.0
[INFO] [2021-04-29 15:43:52] Total Time: 1s
[STOP] [2021-04-29 15:43:52] parse_diff_and_store
[START] [2021-04-29 15:43:52] resolve_keys
[INFO] [2021-04-29 15:44:02] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-29 15:44:02] traits to occurrences...
[INFO] [2021-04-29 15:44:02] traits to nodes (through occurrences)...
[INFO] [2021-04-29 15:44:02] Traits to sex term...
[INFO] [2021-04-29 15:44:02] Traits to lifestage term...
[INFO] [2021-04-29 15:44:02] MetaTraits to traits...
[INFO] [2021-04-29 15:44:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-29 15:44:02] Assocs to occurrences...
[INFO] [2021-04-29 15:44:02] Assocs to nodes...
[INFO] [2021-04-29 15:44:02] Assoc to sex term...
[INFO] [2021-04-29 15:44:02] Assoc to lifestage term...
[INFO] [2021-04-29 15:44:02] MetaAssoc to assocs...
[STOP] [2021-04-29 15:44:02] resolve_keys
[START] [2021-04-29 15:44:02] hold_for_later_1
[STOP] [2021-04-29 15:44:02] hold_for_later_1
[START] [2021-04-29 15:44:02] hold_for_later_2
[STOP] [2021-04-29 15:44:02] hold_for_later_2
[START] [2021-04-29 15:44:02] resolve_missing_parents
[STOP] [2021-04-29 15:44:02] resolve_missing_parents
[START] [2021-04-29 15:44:02] rebuild_nodes
[START] [2021-04-29 15:44:02] Flattener#flatten
[START] [2021-04-29 15:44:02] Flattener#study_resource
[START] [2021-04-29 15:44:02] Flattener#build_ancestry
[STOP] [2021-04-29 15:44:02] Flattener#build_ancestry
[INFO] [2021-04-29 15:44:02] 14 ancestry keys
[START] [2021-04-29 15:44:02] build_node_ancestors
[INFO] [2021-04-29 15:44:02] old ancestors deleted.
[STOP] [2021-04-29 15:44:02] build_node_ancestors
[WARN] [2021-04-29 15:44:02] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-29 15:44:02] Flattener#flatten
[STOP] [2021-04-29 15:44:02] rebuild_nodes
[START] [2021-04-29 15:44:02] resolve_missing_media_owners
[STOP] [2021-04-29 15:44:02] resolve_missing_media_owners
[START] [2021-04-29 15:44:02] sanitize_media_verbatims
[STOP] [2021-04-29 15:44:02] sanitize_media_verbatims
[START] [2021-04-29 15:44:02] queue_downloads
[STOP] [2021-04-29 15:44:02] queue_downloads
[START] [2021-04-29 15:44:02] parse_names
[WARN] [2021-04-29 15:44:02] I see 14 names which still need to be parsed.
[STOP] [2021-04-29 15:44:03] parse_names
[START] [2021-04-29 15:44:03] denormalize_canonical_names_to_nodes
[STOP] [2021-04-29 15:44:03] denormalize_canonical_names_to_nodes
[START] [2021-04-29 15:44:03] match_nodes
[START] [2021-04-29 15:44:03] map_all_nodes_to_pages
[STOP] [2021-04-29 15:44:03] map_all_nodes_to_pages
[INFO] [2021-04-29 15:44:03] ZERO unmatched nodes (of 14)! Nicely done.
[START] [2021-04-29 15:44:03] update_nodes
[STOP] [2021-04-29 15:44:03] update_nodes
[STOP] [2021-04-29 15:44:03] match_nodes
[START] [2021-04-29 15:44:03] reindex_search
[STOP] [2021-04-29 15:44:03] reindex_search
[START] [2021-04-29 15:44:03] normalize_units
[STOP] [2021-04-29 15:44:04] normalize_units
[START] [2021-04-29 15:44:04] calculate_statistics
[2021-04-29 15:44:04] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-29 15:44:04] calculate_statistics
[START] [2021-04-29 15:44:04] complete_harvest_instance
[START] [2021-04-29 15:44:04] overall_tsv_creation
[INFO] [2021-04-29 15:44:04] Processing group of 14 in 1 batches of 10000
[INFO] [2021-04-29 15:45:56] 13 Traits (unfiltered)...
[INFO] [2021-04-29 15:46:32] 13 Traits (filtered)...
[INFO] [2021-04-29 15:46:32] 0 Associations (filtered)...
[INFO] [2021-04-29 15:46:32] 13 metadata added.
[INFO] [2021-04-29 15:46:32] 0 metadata added.
[INFO] [2021-04-29 15:46:58] Average Time: 81.41
[INFO] [2021-04-29 15:46:58] Total Time: 2m55s
[STOP] [2021-04-29 15:46:58] overall_tsv_creation
[INFO] [2021-04-29 15:46:58] Done. Check your files:
[INFO] [2021-04-29 15:46:58] (14 lines) /app/public/data/insect_developme/publish_nodes.tsv
[INFO] [2021-04-29 15:46:58] (14 lines) /app/public/data/insect_developme/publish_scientific_names.tsv
[INFO] [2021-04-29 15:46:58] (14 lines) /app/public/data/insect_developme/publish_traits.tsv
[INFO] [2021-04-29 15:46:58] (14 lines) /app/public/data/insect_developme/publish_metadata.tsv
[STOP] [2021-04-29 15:46:58] complete_harvest_instance
[START] [2021-04-29 15:46:58] completed
[STOP] [2021-04-29 15:46:58] completed
[STOP] [2021-04-29 15:46:58] logged process, took 187.18
Latest Process

29 Apr 15:43 EXITED currently processing 0