Harvest for Baumann et al 1995 Created 11 Jun 14:08

Harvesting Log

# Logfile created on 2020-06-11 14:08:14 -0400 by logger.rb/v1.4.2
[INFO] [2020-06-11 14:08:14] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-11 14:08:16] ## remove_type: ScientificName
[INFO] [2020-06-11 14:08:16] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:08:16] [14:08:16.071] Removed 0 Scientificnames
[INFO] [2020-06-11 14:08:16] ## remove_type: Vernacular
[INFO] [2020-06-11 14:08:16] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:08:16] [14:08:16.074] Removed 0 Vernaculars
[INFO] [2020-06-11 14:08:16] ## remove_type: Article
[INFO] [2020-06-11 14:08:16] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:08:16] [14:08:16.077] Removed 0 Articles
[INFO] [2020-06-11 14:08:16] ## remove_type: Medium
[INFO] [2020-06-11 14:08:16] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:08:16] [14:08:16.081] Removed 0 Media
[INFO] [2020-06-11 14:08:16] ## remove_type: Trait
[INFO] [2020-06-11 14:08:16] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:08:16] [14:08:16.084] Removed 0 Traits
[INFO] [2020-06-11 14:08:16] ## remove_type: MetaTrait
[INFO] [2020-06-11 14:08:16] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:08:16] [14:08:16.087] Removed 0 Metatraits
[INFO] [2020-06-11 14:08:16] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-11 14:08:16] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:08:16] [14:08:16.090] Removed 0 Occurrencemetadata
[INFO] [2020-06-11 14:08:16] ## remove_type: Assoc
[INFO] [2020-06-11 14:08:16] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:08:16] [14:08:16.093] Removed 0 Assocs
[INFO] [2020-06-11 14:08:16] ## remove_type: MetaAssoc
[INFO] [2020-06-11 14:08:16] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:08:16] [14:08:16.095] Removed 0 Metaassocs
[INFO] [2020-06-11 14:08:16] ## remove_type: Identifier
[INFO] [2020-06-11 14:08:16] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:08:16] [14:08:16.098] Removed 0 Identifiers
[INFO] [2020-06-11 14:08:16] ## remove_type: Reference
[INFO] [2020-06-11 14:08:16] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:08:16] [14:08:16.100] Removed 0 References
[INFO] [2020-06-11 14:08:16] ## remove_type: Node
[INFO] [2020-06-11 14:08:16] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:08:16] [14:08:16.122] Removed 0 Nodes
[START] [2020-06-11 14:08:16] logged process
[START] [2020-06-11 14:08:16] Creating resource from OpenData
[START] [2020-06-11 14:08:16] logged process
[START] [2020-06-11 14:08:16] Parse meta.xml file and create formats with fields
[STOP] [2020-06-11 14:08:16] Parse meta.xml file and create formats with fields
[STOP] [2020-06-11 14:08:16] Creating resource from OpenData
[START] [2020-06-11 14:08:16] logged process
[START] [2020-06-11 14:08:16] create_harvest_instance
[STOP] [2020-06-11 14:08:17] create_harvest_instance
[START] [2020-06-11 14:08:17] fetch_files
[STOP] [2020-06-11 14:08:17] fetch_files
[START] [2020-06-11 14:08:17] validate_each_file
[STOP] [2020-06-11 14:08:17] validate_each_file
[START] [2020-06-11 14:08:17] convert_to_csv
[CMD] [2020-06-11 14:08:17] /usr/bin/sort /app/public/converted_csv/baumann_et_al_ba_nodes_21210.csv > /app/public/converted_csv/baumann_et_al_ba_nodes_21210.csv_sorted
[CMD] [2020-06-11 14:08:17] /usr/bin/sort /app/public/converted_csv/baumann_et_al_ba_occurrences_21211.csv > /app/public/converted_csv/baumann_et_al_ba_occurrences_21211.csv_sorted
[CMD] [2020-06-11 14:08:17] /usr/bin/sort /app/public/converted_csv/baumann_et_al_ba_measurements_21212.csv > /app/public/converted_csv/baumann_et_al_ba_measurements_21212.csv_sorted
[STOP] [2020-06-11 14:08:17] convert_to_csv
[START] [2020-06-11 14:08:17] calculate_delta
[CMD] [2020-06-11 14:08:17] echo "0a" > /app/public/diff/baumann_et_al_ba_nodes_21210.diff
[CMD] [2020-06-11 14:08:17] tail -n +1 /app/public/converted_csv/baumann_et_al_ba_nodes_21210.csv >> /app/public/diff/baumann_et_al_ba_nodes_21210.diff
[CMD] [2020-06-11 14:08:17] echo "." >> /app/public/diff/baumann_et_al_ba_nodes_21210.diff
[CMD] [2020-06-11 14:08:17] echo "0a" > /app/public/diff/baumann_et_al_ba_occurrences_21211.diff
[CMD] [2020-06-11 14:08:17] tail -n +1 /app/public/converted_csv/baumann_et_al_ba_occurrences_21211.csv >> /app/public/diff/baumann_et_al_ba_occurrences_21211.diff
[CMD] [2020-06-11 14:08:17] echo "." >> /app/public/diff/baumann_et_al_ba_occurrences_21211.diff
[CMD] [2020-06-11 14:08:17] echo "0a" > /app/public/diff/baumann_et_al_ba_measurements_21212.diff
[CMD] [2020-06-11 14:08:17] tail -n +1 /app/public/converted_csv/baumann_et_al_ba_measurements_21212.csv >> /app/public/diff/baumann_et_al_ba_measurements_21212.diff
[CMD] [2020-06-11 14:08:17] echo "." >> /app/public/diff/baumann_et_al_ba_measurements_21212.diff
[STOP] [2020-06-11 14:08:17] calculate_delta
[START] [2020-06-11 14:08:17] parse_diff_and_store
[INFO] [2020-06-11 14:08:17] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-11 14:08:17] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-11 14:08:17] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-11 14:08:17] Storing 4 ScientificNames
[INFO] [2020-06-11 14:08:17] Processing group of 4 in 1 groups of 1000
[INFO] [2020-06-11 14:08:17] Average Time: 0.0
[INFO] [2020-06-11 14:08:17] Total Time: 1s
[INFO] [2020-06-11 14:08:17] Storing 4 Nodes
[INFO] [2020-06-11 14:08:17] Processing group of 4 in 1 groups of 1000
[INFO] [2020-06-11 14:08:17] Average Time: 0.0
[INFO] [2020-06-11 14:08:17] Total Time: 1s
[INFO] [2020-06-11 14:08:17] Storing 1 Occurrences
[INFO] [2020-06-11 14:08:17] Processing group of 1 in 1 groups of 1000
[INFO] [2020-06-11 14:08:17] Average Time: 0.0
[INFO] [2020-06-11 14:08:17] Total Time: 1s
[INFO] [2020-06-11 14:08:17] Storing 3 Traits
[INFO] [2020-06-11 14:08:17] Processing group of 3 in 1 groups of 1000
[INFO] [2020-06-11 14:08:17] Average Time: 0.0
[INFO] [2020-06-11 14:08:17] Total Time: 1s
[INFO] [2020-06-11 14:08:17] Storing 3 MetaTraits
[INFO] [2020-06-11 14:08:17] Processing group of 3 in 1 groups of 1000
[INFO] [2020-06-11 14:08:17] Average Time: 0.0
[INFO] [2020-06-11 14:08:17] Total Time: 1s
[STOP] [2020-06-11 14:08:17] parse_diff_and_store
[START] [2020-06-11 14:08:17] resolve_keys
[INFO] [2020-06-11 14:08:24] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-11 14:08:24] traits to occurrences...
[INFO] [2020-06-11 14:08:24] traits to nodes (through occurrences)...
[INFO] [2020-06-11 14:08:24] Traits to sex term...
[INFO] [2020-06-11 14:08:24] Traits to lifestage term...
[INFO] [2020-06-11 14:08:24] MetaTraits to traits...
[INFO] [2020-06-11 14:08:24] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-11 14:08:24] Assocs to occurrences...
[INFO] [2020-06-11 14:08:24] Assocs to nodes...
[INFO] [2020-06-11 14:08:24] Assoc to sex term...
[INFO] [2020-06-11 14:08:24] Assoc to lifestage term...
[STOP] [2020-06-11 14:08:24] resolve_keys
[START] [2020-06-11 14:08:24] hold_for_later_1
[STOP] [2020-06-11 14:08:24] hold_for_later_1
[START] [2020-06-11 14:08:24] hold_for_later_2
[STOP] [2020-06-11 14:08:24] hold_for_later_2
[START] [2020-06-11 14:08:24] resolve_missing_parents
[STOP] [2020-06-11 14:08:24] resolve_missing_parents
[START] [2020-06-11 14:08:24] rebuild_nodes
[START] [2020-06-11 14:08:24] Flattener#flatten
[START] [2020-06-11 14:08:24] Flattener#study_resource
[START] [2020-06-11 14:08:24] Flattener#build_ancestry
[STOP] [2020-06-11 14:08:24] Flattener#build_ancestry
[INFO] [2020-06-11 14:08:24] 4 ancestry keys
[START] [2020-06-11 14:08:24] build_node_ancestors
[INFO] [2020-06-11 14:08:24] old ancestors deleted.
[STOP] [2020-06-11 14:08:24] build_node_ancestors
[START] [2020-06-11 14:08:24] Flattener#propagate_ancestor_ids
[STOP] [2020-06-11 14:08:24] Flattener#propagate_ancestor_ids
[STOP] [2020-06-11 14:08:24] Flattener#flatten
[STOP] [2020-06-11 14:08:24] rebuild_nodes
[START] [2020-06-11 14:08:24] resolve_missing_media_owners
[STOP] [2020-06-11 14:08:24] resolve_missing_media_owners
[START] [2020-06-11 14:08:24] sanitize_media_verbatims
[STOP] [2020-06-11 14:08:24] sanitize_media_verbatims
[START] [2020-06-11 14:08:24] queue_downloads
[STOP] [2020-06-11 14:08:24] queue_downloads
[START] [2020-06-11 14:08:24] parse_names
[WARN] [2020-06-11 14:08:24] I see 4 names which still need to be parsed.
[STOP] [2020-06-11 14:08:25] parse_names
[START] [2020-06-11 14:08:25] denormalize_canonical_names_to_nodes
[STOP] [2020-06-11 14:08:25] denormalize_canonical_names_to_nodes
[START] [2020-06-11 14:08:25] match_nodes
[START] [2020-06-11 14:08:26] map_all_nodes_to_pages
[STOP] [2020-06-11 14:08:26] map_all_nodes_to_pages
[INFO] [2020-06-11 14:08:26] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2020-06-11 14:08:26] update_nodes
[STOP] [2020-06-11 14:08:26] update_nodes
[STOP] [2020-06-11 14:08:26] match_nodes
[START] [2020-06-11 14:08:26] reindex_search
[STOP] [2020-06-11 14:08:26] reindex_search
[START] [2020-06-11 14:08:26] normalize_units
[STOP] [2020-06-11 14:08:26] normalize_units
[START] [2020-06-11 14:08:26] calculate_statistics
[STOP] [2020-06-11 14:08:26] calculate_statistics
[START] [2020-06-11 14:08:26] complete_harvest_instance
[START] [2020-06-11 14:08:26] overall_tsv_creation
[INFO] [2020-06-11 14:08:26] Processing group of 4 in 1 batches of 10000
[INFO] [2020-06-11 14:09:16] 1 Traits (unfiltered)...
[INFO] [2020-06-11 14:09:29] 1 Traits (filtered)...
[INFO] [2020-06-11 14:09:29] 0 Associations (filtered)...
[INFO] [2020-06-11 14:10:07] 5 metadata added.
[INFO] [2020-06-11 14:10:07] 0 metadata added.
[INFO] [2020-06-11 14:10:07] Average Time: 72.6
[INFO] [2020-06-11 14:10:07] Total Time: 1m41s
[STOP] [2020-06-11 14:10:07] overall_tsv_creation
[INFO] [2020-06-11 14:10:07] Done. Check your files:
[INFO] [2020-06-11 14:10:07] (4 lines) /app/public/data/baumann_et_al_ba/publish_nodes.tsv
[INFO] [2020-06-11 14:10:07] (6 lines) /app/public/data/baumann_et_al_ba/publish_node_ancestors.tsv
[INFO] [2020-06-11 14:10:07] (4 lines) /app/public/data/baumann_et_al_ba/publish_scientific_names.tsv
[INFO] [2020-06-11 14:10:07] (2 lines) /app/public/data/baumann_et_al_ba/publish_traits.tsv
[INFO] [2020-06-11 14:10:07] (6 lines) /app/public/data/baumann_et_al_ba/publish_metadata.tsv
[STOP] [2020-06-11 14:10:07] complete_harvest_instance
[START] [2020-06-11 14:10:07] completed
[STOP] [2020-06-11 14:10:07] completed
[STOP] [2020-06-11 14:10:07] logged process, took 110.74

Latest Process

11 Jun 14:08 EXITED currently processing 0