Stage:
completed
Fetched:
19 Apr 16:58
Validated:
19 Apr 16:58
Deltas Created
19 Apr 16:58
Units Normalized:
19 Apr 16:58
Ancestry Built:
19 Apr 16:58
Nodes Matched:
19 Apr 16:58
Names Parsed:
19 Apr 16:58
New Models Stored:
19 Apr 16:58
Indexed:
19 Apr 16:58
Completed:
19 Apr 16:59
Time to Harvest:
less than a minute
Harvesting Log
(410 lines)
# Logfile created on 2020-12-08 15:24:45 -0500 by logger.rb/v1.4.2
[START] [2020-12-08 15:24:45] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-08 15:24:45] Creating resource from OpenData
[START] [2020-12-08 15:24:46] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-08 15:24:46] Parse meta.xml file and create formats with fields
[STOP] [2020-12-08 15:24:46] Parse meta.xml file and create formats with fields
[STOP] [2020-12-08 15:24:46] Creating resource from OpenData
[INFO] [2020-12-08 15:25:03] ## HARVEST: type = -harvest
[START] [2020-12-08 15:25:06] logged process: 58bbc42b01abb4c1b2698de049792ffb4b63b979
[START] [2020-12-08 15:25:06] create_harvest_instance
[STOP] [2020-12-08 15:25:08] create_harvest_instance
[START] [2020-12-08 15:25:08] fetch_files
[STOP] [2020-12-08 15:25:08] fetch_files
[START] [2020-12-08 15:25:08] validate_each_file
[STOP] [2020-12-08 15:25:08] validate_each_file
[START] [2020-12-08 15:25:08] convert_to_csv
[CMD] [2020-12-08 15:25:08] /usr/bin/sort /app/public/converted_csv/bringloe_et_al_b_nodes_25303.csv > /app/public/converted_csv/bringloe_et_al_b_nodes_25303.csv_sorted
[CMD] [2020-12-08 15:25:08] /usr/bin/sort /app/public/converted_csv/bringloe_et_al_b_occurrences_25304.csv > /app/public/converted_csv/bringloe_et_al_b_occurrences_25304.csv_sorted
[CMD] [2020-12-08 15:25:08] /usr/bin/sort /app/public/converted_csv/bringloe_et_al_b_measurements_25305.csv > /app/public/converted_csv/bringloe_et_al_b_measurements_25305.csv_sorted
[STOP] [2020-12-08 15:25:08] convert_to_csv
[START] [2020-12-08 15:25:08] calculate_delta
[CMD] [2020-12-08 15:25:08] echo "0a" > /app/public/diff/bringloe_et_al_b_nodes_25303.diff
[CMD] [2020-12-08 15:25:08] tail -n +1 /app/public/converted_csv/bringloe_et_al_b_nodes_25303.csv >> /app/public/diff/bringloe_et_al_b_nodes_25303.diff
[CMD] [2020-12-08 15:25:08] echo "." >> /app/public/diff/bringloe_et_al_b_nodes_25303.diff
[CMD] [2020-12-08 15:25:08] echo "0a" > /app/public/diff/bringloe_et_al_b_occurrences_25304.diff
[CMD] [2020-12-08 15:25:08] tail -n +1 /app/public/converted_csv/bringloe_et_al_b_occurrences_25304.csv >> /app/public/diff/bringloe_et_al_b_occurrences_25304.diff
[CMD] [2020-12-08 15:25:08] echo "." >> /app/public/diff/bringloe_et_al_b_occurrences_25304.diff
[CMD] [2020-12-08 15:25:08] echo "0a" > /app/public/diff/bringloe_et_al_b_measurements_25305.diff
[CMD] [2020-12-08 15:25:08] tail -n +1 /app/public/converted_csv/bringloe_et_al_b_measurements_25305.csv >> /app/public/diff/bringloe_et_al_b_measurements_25305.diff
[CMD] [2020-12-08 15:25:08] echo "." >> /app/public/diff/bringloe_et_al_b_measurements_25305.diff
[STOP] [2020-12-08 15:25:08] calculate_delta
[START] [2020-12-08 15:25:08] parse_diff_and_store
[INFO] [2020-12-08 15:25:08] Loading nodes diff file into memory (true lines)...
[INFO] [2020-12-08 15:25:08] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-12-08 15:25:08] Loading measurements diff file into memory (true lines)...
[INFO] [2020-12-08 15:25:09] Storing 6 ScientificNames
[INFO] [2020-12-08 15:25:09] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-08 15:25:09] Average Time: 0.01
[INFO] [2020-12-08 15:25:09] Total Time: 1s
[INFO] [2020-12-08 15:25:09] Storing 6 Nodes
[INFO] [2020-12-08 15:25:09] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-08 15:25:09] Average Time: 0.01
[INFO] [2020-12-08 15:25:09] Total Time: 1s
[INFO] [2020-12-08 15:25:09] Storing 6 Occurrences
[INFO] [2020-12-08 15:25:09] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-08 15:25:09] Average Time: 0.0
[INFO] [2020-12-08 15:25:09] Total Time: 1s
[INFO] [2020-12-08 15:25:09] Storing 12 Traits
[INFO] [2020-12-08 15:25:09] Processing group of 12 in 1 groups of 1000
[INFO] [2020-12-08 15:25:09] Average Time: 0.01
[INFO] [2020-12-08 15:25:09] Total Time: 1s
[INFO] [2020-12-08 15:25:09] Storing 6 MetaTraits
[INFO] [2020-12-08 15:25:09] Processing group of 6 in 1 groups of 1000
[INFO] [2020-12-08 15:25:09] Average Time: 0.0
[INFO] [2020-12-08 15:25:09] Total Time: 1s
[STOP] [2020-12-08 15:25:09] parse_diff_and_store
[START] [2020-12-08 15:25:09] resolve_keys
[INFO] [2020-12-08 15:25:14] Occurrences to nodes (through scientific_names)...
[INFO] [2020-12-08 15:25:14] traits to occurrences...
[INFO] [2020-12-08 15:25:14] traits to nodes (through occurrences)...
[INFO] [2020-12-08 15:25:14] Traits to sex term...
[INFO] [2020-12-08 15:25:14] Traits to lifestage term...
[INFO] [2020-12-08 15:25:14] MetaTraits to traits...
[INFO] [2020-12-08 15:25:14] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-12-08 15:25:14] Assocs to occurrences...
[INFO] [2020-12-08 15:25:14] Assocs to nodes...
[INFO] [2020-12-08 15:25:14] Assoc to sex term...
[INFO] [2020-12-08 15:25:14] Assoc to lifestage term...
[INFO] [2020-12-08 15:25:14] MetaAssoc to assocs...
[STOP] [2020-12-08 15:25:14] resolve_keys
[START] [2020-12-08 15:25:14] hold_for_later_1
[STOP] [2020-12-08 15:25:14] hold_for_later_1
[START] [2020-12-08 15:25:14] hold_for_later_2
[STOP] [2020-12-08 15:25:14] hold_for_later_2
[START] [2020-12-08 15:25:14] resolve_missing_parents
[STOP] [2020-12-08 15:25:14] resolve_missing_parents
[START] [2020-12-08 15:25:14] rebuild_nodes
[START] [2020-12-08 15:25:14] Flattener#flatten
[START] [2020-12-08 15:25:14] Flattener#study_resource
[START] [2020-12-08 15:25:14] Flattener#build_ancestry
[STOP] [2020-12-08 15:25:14] Flattener#build_ancestry
[INFO] [2020-12-08 15:25:14] 6 ancestry keys
[START] [2020-12-08 15:25:14] build_node_ancestors
[INFO] [2020-12-08 15:25:14] old ancestors deleted.
[STOP] [2020-12-08 15:25:15] build_node_ancestors
[WARN] [2020-12-08 15:25:15] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-12-08 15:25:15] Flattener#flatten
[STOP] [2020-12-08 15:25:15] rebuild_nodes
[START] [2020-12-08 15:25:15] resolve_missing_media_owners
[STOP] [2020-12-08 15:25:15] resolve_missing_media_owners
[START] [2020-12-08 15:25:15] sanitize_media_verbatims
[STOP] [2020-12-08 15:25:15] sanitize_media_verbatims
[START] [2020-12-08 15:25:15] queue_downloads
[STOP] [2020-12-08 15:25:15] queue_downloads
[START] [2020-12-08 15:25:15] parse_names
[WARN] [2020-12-08 15:25:15] I see 6 names which still need to be parsed.
[STOP] [2020-12-08 15:25:16] parse_names
[START] [2020-12-08 15:25:16] denormalize_canonical_names_to_nodes
[STOP] [2020-12-08 15:25:16] denormalize_canonical_names_to_nodes
[START] [2020-12-08 15:25:16] match_nodes
[START] [2020-12-08 15:25:16] map_all_nodes_to_pages
[STOP] [2020-12-08 15:25:16] map_all_nodes_to_pages
[INFO] [2020-12-08 15:25:16] ZERO unmatched nodes (of 6)! Nicely done.
[START] [2020-12-08 15:25:16] update_nodes
[STOP] [2020-12-08 15:25:16] update_nodes
[STOP] [2020-12-08 15:25:16] match_nodes
[START] [2020-12-08 15:25:16] reindex_search
[STOP] [2020-12-08 15:25:16] reindex_search
[START] [2020-12-08 15:25:16] normalize_units
[STOP] [2020-12-08 15:25:16] normalize_units
[START] [2020-12-08 15:25:16] calculate_statistics
[2020-12-08 15:25:16] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-12-08 15:25:16] calculate_statistics
[START] [2020-12-08 15:25:16] complete_harvest_instance
[START] [2020-12-08 15:25:16] overall_tsv_creation
[INFO] [2020-12-08 15:25:16] Processing group of 6 in 1 batches of 10000
[INFO] [2020-12-08 15:25:55] 6 Traits (unfiltered)...
[INFO] [2020-12-08 15:26:33] 6 Traits (filtered)...
[INFO] [2020-12-08 15:26:33] 0 Associations (filtered)...
[INFO] [2020-12-08 15:26:33] 12 metadata added.
[INFO] [2020-12-08 15:26:33] 0 metadata added.
[INFO] [2020-12-08 15:26:33] Average Time: 54.34
[INFO] [2020-12-08 15:26:33] Total Time: 1m18s
[STOP] [2020-12-08 15:26:33] overall_tsv_creation
[INFO] [2020-12-08 15:26:33] Done. Check your files:
[INFO] [2020-12-08 15:26:33] (6 lines) /app/public/data/bringloe_et_al_b/publish_nodes.tsv
[INFO] [2020-12-08 15:26:33] (6 lines) /app/public/data/bringloe_et_al_b/publish_scientific_names.tsv
[INFO] [2020-12-08 15:26:33] (7 lines) /app/public/data/bringloe_et_al_b/publish_traits.tsv
[INFO] [2020-12-08 15:26:33] (13 lines) /app/public/data/bringloe_et_al_b/publish_metadata.tsv
[STOP] [2020-12-08 15:26:33] complete_harvest_instance
[START] [2020-12-08 15:26:33] completed
[STOP] [2020-12-08 15:26:33] completed
[STOP] [2020-12-08 15:26:33] logged process, took 86.58
[INFO] [2021-04-19 16:47:47] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2021-04-19 16:58:06] ## remove_type: ScientificName
[INFO] [2021-04-19 16:58:06] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 16:58:06] [16:58:06.981] Removed 6 Scientificnames
[INFO] [2021-04-19 16:58:06] ## remove_type: Vernacular
[INFO] [2021-04-19 16:58:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:58:06] [16:58:06.982] Removed 0 Vernaculars
[INFO] [2021-04-19 16:58:06] ## remove_type: Article
[INFO] [2021-04-19 16:58:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:58:06] [16:58:06.983] Removed 0 Articles
[INFO] [2021-04-19 16:58:06] ## remove_type: Medium
[INFO] [2021-04-19 16:58:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:58:06] [16:58:06.985] Removed 0 Media
[INFO] [2021-04-19 16:58:06] ## remove_type: Trait
[INFO] [2021-04-19 16:58:06] ++ Calling delete_all on 12 instances...
[INFO] [2021-04-19 16:58:06] [16:58:06.987] Removed 12 Traits
[INFO] [2021-04-19 16:58:06] ## remove_type: MetaTrait
[INFO] [2021-04-19 16:58:06] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 16:58:06] [16:58:06.989] Removed 6 Metatraits
[INFO] [2021-04-19 16:58:06] ## remove_type: OccurrenceMetadatum
[INFO] [2021-04-19 16:58:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:58:06] [16:58:06.991] Removed 0 Occurrencemetadata
[INFO] [2021-04-19 16:58:06] ## remove_type: Assoc
[INFO] [2021-04-19 16:58:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:58:06] [16:58:06.992] Removed 0 Assocs
[INFO] [2021-04-19 16:58:06] ## remove_type: MetaAssoc
[INFO] [2021-04-19 16:58:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:58:06] [16:58:06.993] Removed 0 Metaassocs
[INFO] [2021-04-19 16:58:06] ## remove_type: Identifier
[INFO] [2021-04-19 16:58:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:58:06] [16:58:06.994] Removed 0 Identifiers
[INFO] [2021-04-19 16:58:06] ## remove_type: Reference
[INFO] [2021-04-19 16:58:06] ++ Calling delete_all on 0 instances...
[INFO] [2021-04-19 16:58:06] [16:58:06.996] Removed 0 References
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] Starting batch with ID 86121272...
[INFO] [2021-04-19 16:58:07] ## remove_type: Node
[INFO] [2021-04-19 16:58:07] ++ Calling delete_all on 6 instances...
[INFO] [2021-04-19 16:58:07] [16:58:07.590] Removed 6 Nodes
[START] [2021-04-19 16:58:07] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:58:07] Creating resource from OpenData
[START] [2021-04-19 16:58:07] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:58:07] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:58:07] Parse meta.xml file and create formats with fields
[STOP] [2021-04-19 16:58:07] Creating resource from OpenData
[START] [2021-04-19 16:58:07] logged process: 5ecc716a6a5541910d0c854f5a0c8d1651b82ad0 Improved MetaXml.ignore and added publisher to media (ignored)
[START] [2021-04-19 16:58:07] create_harvest_instance
[INFO] [2021-04-19 16:58:07] Created harvest instance #3811
[STOP] [2021-04-19 16:58:07] create_harvest_instance
[START] [2021-04-19 16:58:07] fetch_files
[STOP] [2021-04-19 16:58:07] fetch_files
[START] [2021-04-19 16:58:07] validate_each_file
[INFO] [2021-04-19 16:58:08] Looping over 3 formats...
[INFO] [2021-04-19 16:58:08] ...nodes (/app/public/data/bringloe_et_al_b/taxa.txt)
[INFO] [2021-04-19 16:58:08] Valid: /app/public/converted_csv/bringloe_et_al_b_nodes_3811.csv (6 lines)
[INFO] [2021-04-19 16:58:08] ...occurrences (/app/public/data/bringloe_et_al_b/occurrences.txt)
[INFO] [2021-04-19 16:58:08] Valid: /app/public/converted_csv/bringloe_et_al_b_occurrences_3811.csv (6 lines)
[INFO] [2021-04-19 16:58:08] ...measurements (/app/public/data/bringloe_et_al_b/measurementsorfacts.txt)
[INFO] [2021-04-19 16:58:08] Valid: /app/public/converted_csv/bringloe_et_al_b_measurements_3811.csv (12 lines)
[STOP] [2021-04-19 16:58:08] validate_each_file
[START] [2021-04-19 16:58:08] convert_to_csv
[INFO] [2021-04-19 16:58:08] Looping over 3 formats...
[INFO] [2021-04-19 16:58:08] ...nodes (/app/public/data/bringloe_et_al_b/taxa.txt)
[CMD] [2021-04-19 16:58:08] /usr/bin/sort /app/public/converted_csv/bringloe_et_al_b_nodes_3811.csv > /app/public/converted_csv/bringloe_et_al_b_nodes_3811.csv_sorted
[INFO] [2021-04-19 16:58:08] Converted: /app/public/converted_csv/bringloe_et_al_b_nodes_3811.csv (6 lines)
[INFO] [2021-04-19 16:58:08] ...occurrences (/app/public/data/bringloe_et_al_b/occurrences.txt)
[CMD] [2021-04-19 16:58:08] /usr/bin/sort /app/public/converted_csv/bringloe_et_al_b_occurrences_3811.csv > /app/public/converted_csv/bringloe_et_al_b_occurrences_3811.csv_sorted
[INFO] [2021-04-19 16:58:08] Converted: /app/public/converted_csv/bringloe_et_al_b_occurrences_3811.csv (6 lines)
[INFO] [2021-04-19 16:58:08] ...measurements (/app/public/data/bringloe_et_al_b/measurementsorfacts.txt)
[CMD] [2021-04-19 16:58:08] /usr/bin/sort /app/public/converted_csv/bringloe_et_al_b_measurements_3811.csv > /app/public/converted_csv/bringloe_et_al_b_measurements_3811.csv_sorted
[INFO] [2021-04-19 16:58:08] Converted: /app/public/converted_csv/bringloe_et_al_b_measurements_3811.csv (12 lines)
[STOP] [2021-04-19 16:58:08] convert_to_csv
[START] [2021-04-19 16:58:08] calculate_delta
[INFO] [2021-04-19 16:58:08] Looping over 3 formats...
[INFO] [2021-04-19 16:58:08] ...nodes (/app/public/data/bringloe_et_al_b/taxa.txt)
[CMD] [2021-04-19 16:58:08] echo "0a" > /app/public/diff/bringloe_et_al_b_nodes_3811.diff
[CMD] [2021-04-19 16:58:08] tail -n +1 /app/public/converted_csv/bringloe_et_al_b_nodes_3811.csv >> /app/public/diff/bringloe_et_al_b_nodes_3811.diff
[CMD] [2021-04-19 16:58:08] echo "." >> /app/public/diff/bringloe_et_al_b_nodes_3811.diff
[INFO] [2021-04-19 16:58:08] Created diff: /app/public/diff/bringloe_et_al_b_nodes_3811.diff (8 lines)
[INFO] [2021-04-19 16:58:08] ...occurrences (/app/public/data/bringloe_et_al_b/occurrences.txt)
[CMD] [2021-04-19 16:58:08] echo "0a" > /app/public/diff/bringloe_et_al_b_occurrences_3811.diff
[CMD] [2021-04-19 16:58:08] tail -n +1 /app/public/converted_csv/bringloe_et_al_b_occurrences_3811.csv >> /app/public/diff/bringloe_et_al_b_occurrences_3811.diff
[CMD] [2021-04-19 16:58:08] echo "." >> /app/public/diff/bringloe_et_al_b_occurrences_3811.diff
[INFO] [2021-04-19 16:58:08] Created diff: /app/public/diff/bringloe_et_al_b_occurrences_3811.diff (8 lines)
[INFO] [2021-04-19 16:58:08] ...measurements (/app/public/data/bringloe_et_al_b/measurementsorfacts.txt)
[CMD] [2021-04-19 16:58:08] echo "0a" > /app/public/diff/bringloe_et_al_b_measurements_3811.diff
[CMD] [2021-04-19 16:58:08] tail -n +1 /app/public/converted_csv/bringloe_et_al_b_measurements_3811.csv >> /app/public/diff/bringloe_et_al_b_measurements_3811.diff
[CMD] [2021-04-19 16:58:08] echo "." >> /app/public/diff/bringloe_et_al_b_measurements_3811.diff
[INFO] [2021-04-19 16:58:08] Created diff: /app/public/diff/bringloe_et_al_b_measurements_3811.diff (14 lines)
[STOP] [2021-04-19 16:58:08] calculate_delta
[START] [2021-04-19 16:58:08] parse_diff_and_store
[INFO] [2021-04-19 16:58:08] Handling diff: /app/public/diff/bringloe_et_al_b_nodes_3811.diff (8 lines)
[INFO] [2021-04-19 16:58:08] Loading nodes diff file into memory (8 /app/public/diff/bringloe_et_al_b_nodes_3811.diff lines)...
[INFO] [2021-04-19 16:58:08] Handling diff: /app/public/diff/bringloe_et_al_b_occurrences_3811.diff (8 lines)
[INFO] [2021-04-19 16:58:08] Loading occurrences diff file into memory (8 /app/public/diff/bringloe_et_al_b_occurrences_3811.diff lines)...
[INFO] [2021-04-19 16:58:08] Handling diff: /app/public/diff/bringloe_et_al_b_measurements_3811.diff (14 lines)
[INFO] [2021-04-19 16:58:08] Loading measurements diff file into memory (14 /app/public/diff/bringloe_et_al_b_measurements_3811.diff lines)...
[INFO] [2021-04-19 16:58:08] Storing 6 ScientificNames
[INFO] [2021-04-19 16:58:08] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 16:58:08] Average Time: 0.0
[INFO] [2021-04-19 16:58:08] Total Time: 1s
[INFO] [2021-04-19 16:58:08] Storing 6 Nodes
[INFO] [2021-04-19 16:58:08] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 16:58:08] Average Time: 0.0
[INFO] [2021-04-19 16:58:08] Total Time: 1s
[INFO] [2021-04-19 16:58:08] Storing 6 Occurrences
[INFO] [2021-04-19 16:58:08] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 16:58:08] Average Time: 0.0
[INFO] [2021-04-19 16:58:08] Total Time: 1s
[INFO] [2021-04-19 16:58:08] Storing 12 Traits
[INFO] [2021-04-19 16:58:08] Processing group of 12 in 1 groups of 1000
[INFO] [2021-04-19 16:58:08] Average Time: 0.01
[INFO] [2021-04-19 16:58:08] Total Time: 1s
[INFO] [2021-04-19 16:58:08] Storing 6 MetaTraits
[INFO] [2021-04-19 16:58:08] Processing group of 6 in 1 groups of 1000
[INFO] [2021-04-19 16:58:08] Average Time: 0.0
[INFO] [2021-04-19 16:58:08] Total Time: 1s
[STOP] [2021-04-19 16:58:08] parse_diff_and_store
[START] [2021-04-19 16:58:08] resolve_keys
[INFO] [2021-04-19 16:58:14] Occurrences to nodes (through scientific_names)...
[INFO] [2021-04-19 16:58:14] traits to occurrences...
[INFO] [2021-04-19 16:58:14] traits to nodes (through occurrences)...
[INFO] [2021-04-19 16:58:14] Traits to sex term...
[INFO] [2021-04-19 16:58:14] Traits to lifestage term...
[INFO] [2021-04-19 16:58:14] MetaTraits to traits...
[INFO] [2021-04-19 16:58:14] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2021-04-19 16:58:14] Assocs to occurrences...
[INFO] [2021-04-19 16:58:14] Assocs to nodes...
[INFO] [2021-04-19 16:58:14] Assoc to sex term...
[INFO] [2021-04-19 16:58:14] Assoc to lifestage term...
[INFO] [2021-04-19 16:58:14] MetaAssoc to assocs...
[STOP] [2021-04-19 16:58:14] resolve_keys
[START] [2021-04-19 16:58:14] hold_for_later_1
[STOP] [2021-04-19 16:58:14] hold_for_later_1
[START] [2021-04-19 16:58:14] hold_for_later_2
[STOP] [2021-04-19 16:58:14] hold_for_later_2
[START] [2021-04-19 16:58:14] resolve_missing_parents
[STOP] [2021-04-19 16:58:14] resolve_missing_parents
[START] [2021-04-19 16:58:14] rebuild_nodes
[START] [2021-04-19 16:58:14] Flattener#flatten
[START] [2021-04-19 16:58:14] Flattener#study_resource
[START] [2021-04-19 16:58:14] Flattener#build_ancestry
[STOP] [2021-04-19 16:58:14] Flattener#build_ancestry
[INFO] [2021-04-19 16:58:14] 6 ancestry keys
[START] [2021-04-19 16:58:14] build_node_ancestors
[INFO] [2021-04-19 16:58:14] old ancestors deleted.
[STOP] [2021-04-19 16:58:14] build_node_ancestors
[WARN] [2021-04-19 16:58:14] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2021-04-19 16:58:14] Flattener#flatten
[STOP] [2021-04-19 16:58:14] rebuild_nodes
[START] [2021-04-19 16:58:14] resolve_missing_media_owners
[STOP] [2021-04-19 16:58:14] resolve_missing_media_owners
[START] [2021-04-19 16:58:14] sanitize_media_verbatims
[STOP] [2021-04-19 16:58:14] sanitize_media_verbatims
[START] [2021-04-19 16:58:14] queue_downloads
[STOP] [2021-04-19 16:58:14] queue_downloads
[START] [2021-04-19 16:58:14] parse_names
[WARN] [2021-04-19 16:58:14] I see 6 names which still need to be parsed.
[STOP] [2021-04-19 16:58:15] parse_names
[START] [2021-04-19 16:58:15] denormalize_canonical_names_to_nodes
[STOP] [2021-04-19 16:58:15] denormalize_canonical_names_to_nodes
[START] [2021-04-19 16:58:15] match_nodes
[START] [2021-04-19 16:58:15] map_all_nodes_to_pages
[STOP] [2021-04-19 16:58:15] map_all_nodes_to_pages
[INFO] [2021-04-19 16:58:15] ZERO unmatched nodes (of 6)! Nicely done.
[START] [2021-04-19 16:58:15] update_nodes
[STOP] [2021-04-19 16:58:15] update_nodes
[STOP] [2021-04-19 16:58:15] match_nodes
[START] [2021-04-19 16:58:15] reindex_search
[STOP] [2021-04-19 16:58:15] reindex_search
[START] [2021-04-19 16:58:15] normalize_units
[STOP] [2021-04-19 16:58:15] normalize_units
[START] [2021-04-19 16:58:15] calculate_statistics
[2021-04-19 16:58:15] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2021-04-19 16:58:15] calculate_statistics
[START] [2021-04-19 16:58:15] complete_harvest_instance
[START] [2021-04-19 16:58:15] overall_tsv_creation
[INFO] [2021-04-19 16:58:15] Processing group of 6 in 1 batches of 10000
[INFO] [2021-04-19 16:58:51] 6 Traits (unfiltered)...
[INFO] [2021-04-19 16:59:25] 6 Traits (filtered)...
[INFO] [2021-04-19 16:59:25] 0 Associations (filtered)...
[INFO] [2021-04-19 16:59:25] 6 metadata added.
[INFO] [2021-04-19 16:59:25] 0 metadata added.
[INFO] [2021-04-19 16:59:51] Average Time: 71.66
[INFO] [2021-04-19 16:59:51] Total Time: 1m36s
[STOP] [2021-04-19 16:59:51] overall_tsv_creation
[INFO] [2021-04-19 16:59:51] Done. Check your files:
[INFO] [2021-04-19 16:59:51] (6 lines) /app/public/data/bringloe_et_al_b/publish_nodes.tsv
[INFO] [2021-04-19 16:59:51] (6 lines) /app/public/data/bringloe_et_al_b/publish_scientific_names.tsv
[INFO] [2021-04-19 16:59:51] (7 lines) /app/public/data/bringloe_et_al_b/publish_traits.tsv
[INFO] [2021-04-19 16:59:51] (7 lines) /app/public/data/bringloe_et_al_b/publish_metadata.tsv
[STOP] [2021-04-19 16:59:51] complete_harvest_instance
[START] [2021-04-19 16:59:51] completed
[STOP] [2021-04-19 16:59:51] completed
[STOP] [2021-04-19 16:59:51] logged process, took 103.33
Latest Process