Harvest for Schaefer and Summers 2005 Created 22 Jul 15:05

Stage: completed
Fetched: 22 Jul 15:05
Validated: 22 Jul 15:05
Deltas Created 22 Jul 15:05
Units Normalized: 22 Jul 15:05
Ancestry Built: 22 Jul 15:05
Nodes Matched: 22 Jul 15:05
Names Parsed: 22 Jul 15:05
New Models Stored: 22 Jul 15:05
Indexed: 22 Jul 15:05
Completed: 22 Jul 15:07
Time to Harvest: less than a minute
Harvesting Log

(174 lines)
# Logfile created on 2020-07-22 13:00:34 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 13:00:34] logged process
[START] [2020-07-22 13:00:34] Creating resource from OpenData
[START] [2020-07-22 13:00:34] logged process
[START] [2020-07-22 13:00:34] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 13:00:35] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 13:00:35] Creating resource from OpenData
[INFO] [2020-07-22 15:05:44] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-07-22 15:05:45] ## remove_type: ScientificName
[INFO] [2020-07-22 15:05:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:05:45] [15:05:45.893] Removed 0 Scientificnames
[INFO] [2020-07-22 15:05:45] ## remove_type: Vernacular
[INFO] [2020-07-22 15:05:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:05:45] [15:05:45.895] Removed 0 Vernaculars
[INFO] [2020-07-22 15:05:45] ## remove_type: Article
[INFO] [2020-07-22 15:05:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:05:45] [15:05:45.899] Removed 0 Articles
[INFO] [2020-07-22 15:05:45] ## remove_type: Medium
[INFO] [2020-07-22 15:05:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:05:45] [15:05:45.902] Removed 0 Media
[INFO] [2020-07-22 15:05:45] ## remove_type: Trait
[INFO] [2020-07-22 15:05:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:05:45] [15:05:45.905] Removed 0 Traits
[INFO] [2020-07-22 15:05:45] ## remove_type: MetaTrait
[INFO] [2020-07-22 15:05:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:05:45] [15:05:45.907] Removed 0 Metatraits
[INFO] [2020-07-22 15:05:45] ## remove_type: OccurrenceMetadatum
[INFO] [2020-07-22 15:05:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:05:45] [15:05:45.909] Removed 0 Occurrencemetadata
[INFO] [2020-07-22 15:05:45] ## remove_type: Assoc
[INFO] [2020-07-22 15:05:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:05:45] [15:05:45.912] Removed 0 Assocs
[INFO] [2020-07-22 15:05:45] ## remove_type: MetaAssoc
[INFO] [2020-07-22 15:05:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:05:45] [15:05:45.915] Removed 0 Metaassocs
[INFO] [2020-07-22 15:05:45] ## remove_type: Identifier
[INFO] [2020-07-22 15:05:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:05:45] [15:05:45.917] Removed 0 Identifiers
[INFO] [2020-07-22 15:05:45] ## remove_type: Reference
[INFO] [2020-07-22 15:05:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:05:45] [15:05:45.919] Removed 0 References
[INFO] [2020-07-22 15:05:45] ## remove_type: Node
[INFO] [2020-07-22 15:05:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-07-22 15:05:45] [15:05:45.953] Removed 0 Nodes
[START] [2020-07-22 15:05:46] logged process
[START] [2020-07-22 15:05:46] Creating resource from OpenData
[START] [2020-07-22 15:05:46] logged process
[START] [2020-07-22 15:05:46] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:05:46] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:05:46] Creating resource from OpenData
[START] [2020-07-22 15:05:46] logged process
[START] [2020-07-22 15:05:46] create_harvest_instance
[STOP] [2020-07-22 15:05:47] create_harvest_instance
[START] [2020-07-22 15:05:47] fetch_files
[STOP] [2020-07-22 15:05:47] fetch_files
[START] [2020-07-22 15:05:47] validate_each_file
[STOP] [2020-07-22 15:05:47] validate_each_file
[START] [2020-07-22 15:05:47] convert_to_csv
[CMD] [2020-07-22 15:05:47] /usr/bin/sort /app/public/converted_csv/biewener_biewene_nodes_22036.csv > /app/public/converted_csv/biewener_biewene_nodes_22036.csv_sorted
[CMD] [2020-07-22 15:05:47] /usr/bin/sort /app/public/converted_csv/biewener_biewene_occurrences_22037.csv > /app/public/converted_csv/biewener_biewene_occurrences_22037.csv_sorted
[CMD] [2020-07-22 15:05:47] /usr/bin/sort /app/public/converted_csv/biewener_biewene_measurements_22038.csv > /app/public/converted_csv/biewener_biewene_measurements_22038.csv_sorted
[STOP] [2020-07-22 15:05:47] convert_to_csv
[START] [2020-07-22 15:05:47] calculate_delta
[CMD] [2020-07-22 15:05:47] echo "0a" > /app/public/diff/biewener_biewene_nodes_22036.diff
[CMD] [2020-07-22 15:05:47] tail -n +1 /app/public/converted_csv/biewener_biewene_nodes_22036.csv >> /app/public/diff/biewener_biewene_nodes_22036.diff
[CMD] [2020-07-22 15:05:47] echo "." >> /app/public/diff/biewener_biewene_nodes_22036.diff
[CMD] [2020-07-22 15:05:47] echo "0a" > /app/public/diff/biewener_biewene_occurrences_22037.diff
[CMD] [2020-07-22 15:05:47] tail -n +1 /app/public/converted_csv/biewener_biewene_occurrences_22037.csv >> /app/public/diff/biewener_biewene_occurrences_22037.diff
[CMD] [2020-07-22 15:05:47] echo "." >> /app/public/diff/biewener_biewene_occurrences_22037.diff
[CMD] [2020-07-22 15:05:47] echo "0a" > /app/public/diff/biewener_biewene_measurements_22038.diff
[CMD] [2020-07-22 15:05:47] tail -n +1 /app/public/converted_csv/biewener_biewene_measurements_22038.csv >> /app/public/diff/biewener_biewene_measurements_22038.diff
[CMD] [2020-07-22 15:05:47] echo "." >> /app/public/diff/biewener_biewene_measurements_22038.diff
[STOP] [2020-07-22 15:05:47] calculate_delta
[START] [2020-07-22 15:05:47] parse_diff_and_store
[INFO] [2020-07-22 15:05:47] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 15:05:47] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 15:05:47] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 15:05:47] Storing 5 ScientificNames
[INFO] [2020-07-22 15:05:47] Processing group of 5 in 1 groups of 1000
[INFO] [2020-07-22 15:05:47] Average Time: 0.0
[INFO] [2020-07-22 15:05:47] Total Time: 1s
[INFO] [2020-07-22 15:05:47] Storing 5 Nodes
[INFO] [2020-07-22 15:05:47] Processing group of 5 in 1 groups of 1000
[INFO] [2020-07-22 15:05:47] Average Time: 0.0
[INFO] [2020-07-22 15:05:47] Total Time: 1s
[INFO] [2020-07-22 15:05:47] Storing 5 Occurrences
[INFO] [2020-07-22 15:05:47] Processing group of 5 in 1 groups of 1000
[INFO] [2020-07-22 15:05:47] Average Time: 0.0
[INFO] [2020-07-22 15:05:47] Total Time: 1s
[INFO] [2020-07-22 15:05:47] Storing 10 Traits
[INFO] [2020-07-22 15:05:47] Processing group of 10 in 1 groups of 1000
[INFO] [2020-07-22 15:05:47] Average Time: 0.0
[INFO] [2020-07-22 15:05:47] Total Time: 1s
[INFO] [2020-07-22 15:05:47] Storing 10 MetaTraits
[INFO] [2020-07-22 15:05:47] Processing group of 10 in 1 groups of 1000
[INFO] [2020-07-22 15:05:47] Average Time: 0.0
[INFO] [2020-07-22 15:05:47] Total Time: 1s
[STOP] [2020-07-22 15:05:47] parse_diff_and_store
[START] [2020-07-22 15:05:47] resolve_keys
[INFO] [2020-07-22 15:05:54] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 15:05:54] traits to occurrences...
[INFO] [2020-07-22 15:05:54] traits to nodes (through occurrences)...
[INFO] [2020-07-22 15:05:54] Traits to sex term...
[INFO] [2020-07-22 15:05:54] Traits to lifestage term...
[INFO] [2020-07-22 15:05:54] MetaTraits to traits...
[INFO] [2020-07-22 15:05:54] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 15:05:54] Assocs to occurrences...
[INFO] [2020-07-22 15:05:54] Assocs to nodes...
[INFO] [2020-07-22 15:05:54] Assoc to sex term...
[INFO] [2020-07-22 15:05:54] Assoc to lifestage term...
[STOP] [2020-07-22 15:05:54] resolve_keys
[START] [2020-07-22 15:05:54] hold_for_later_1
[STOP] [2020-07-22 15:05:54] hold_for_later_1
[START] [2020-07-22 15:05:54] hold_for_later_2
[STOP] [2020-07-22 15:05:54] hold_for_later_2
[START] [2020-07-22 15:05:54] resolve_missing_parents
[STOP] [2020-07-22 15:05:54] resolve_missing_parents
[START] [2020-07-22 15:05:54] rebuild_nodes
[START] [2020-07-22 15:05:54] Flattener#flatten
[START] [2020-07-22 15:05:54] Flattener#study_resource
[START] [2020-07-22 15:05:54] Flattener#build_ancestry
[STOP] [2020-07-22 15:05:54] Flattener#build_ancestry
[INFO] [2020-07-22 15:05:54] 5 ancestry keys
[START] [2020-07-22 15:05:54] build_node_ancestors
[INFO] [2020-07-22 15:05:54] old ancestors deleted.
[STOP] [2020-07-22 15:05:54] build_node_ancestors
[WARN] [2020-07-22 15:05:54] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 15:05:54] Flattener#flatten
[STOP] [2020-07-22 15:05:54] rebuild_nodes
[START] [2020-07-22 15:05:54] resolve_missing_media_owners
[STOP] [2020-07-22 15:05:54] resolve_missing_media_owners
[START] [2020-07-22 15:05:54] sanitize_media_verbatims
[STOP] [2020-07-22 15:05:54] sanitize_media_verbatims
[START] [2020-07-22 15:05:54] queue_downloads
[STOP] [2020-07-22 15:05:54] queue_downloads
[START] [2020-07-22 15:05:54] parse_names
[WARN] [2020-07-22 15:05:54] I see 5 names which still need to be parsed.
[STOP] [2020-07-22 15:05:55] parse_names
[START] [2020-07-22 15:05:55] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 15:05:55] denormalize_canonical_names_to_nodes
[START] [2020-07-22 15:05:55] match_nodes
[START] [2020-07-22 15:05:55] map_all_nodes_to_pages
[STOP] [2020-07-22 15:05:55] map_all_nodes_to_pages
[INFO] [2020-07-22 15:05:55] ZERO unmatched nodes (of 5)! Nicely done.
[START] [2020-07-22 15:05:55] update_nodes
[STOP] [2020-07-22 15:05:55] update_nodes
[STOP] [2020-07-22 15:05:55] match_nodes
[START] [2020-07-22 15:05:55] reindex_search
[STOP] [2020-07-22 15:05:55] reindex_search
[START] [2020-07-22 15:05:55] normalize_units
[STOP] [2020-07-22 15:05:55] normalize_units
[START] [2020-07-22 15:05:55] calculate_statistics
[2020-07-22 15:05:55] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 15:05:55] calculate_statistics
[START] [2020-07-22 15:05:55] complete_harvest_instance
[START] [2020-07-22 15:05:55] overall_tsv_creation
[INFO] [2020-07-22 15:05:55] Processing group of 5 in 1 batches of 10000
[INFO] [2020-07-22 15:06:45] 5 Traits (unfiltered)...
[INFO] [2020-07-22 15:07:21] 5 Traits (filtered)...
[INFO] [2020-07-22 15:07:21] 0 Associations (filtered)...
[INFO] [2020-07-22 15:07:21] 15 metadata added.
[INFO] [2020-07-22 15:07:21] 0 metadata added.
[INFO] [2020-07-22 15:07:21] Average Time: 58.23
[INFO] [2020-07-22 15:07:21] Total Time: 1m26s
[STOP] [2020-07-22 15:07:21] overall_tsv_creation
[INFO] [2020-07-22 15:07:21] Done. Check your files:
[INFO] [2020-07-22 15:07:21] (5 lines) /app/public/data/biewener_biewene/publish_nodes.tsv
[INFO] [2020-07-22 15:07:21] (5 lines) /app/public/data/biewener_biewene/publish_scientific_names.tsv
[INFO] [2020-07-22 15:07:21] (6 lines) /app/public/data/biewener_biewene/publish_traits.tsv
[INFO] [2020-07-22 15:07:21] (6 lines) /app/public/data/biewener_biewene/publish_metadata.tsv
[STOP] [2020-07-22 15:07:21] complete_harvest_instance
[START] [2020-07-22 15:07:21] completed
[STOP] [2020-07-22 15:07:21] completed
[STOP] [2020-07-22 15:07:21] logged process, took 95.07
Latest Process

22 Jul 15:05 EXITED currently processing 0