Harvest for Trova et al 1994 Created 11 Jun 14:05

Harvesting Log

# Logfile created on 2020-06-11 14:00:41 -0400 by logger.rb/v1.4.2
[INFO] [2020-06-11 14:00:41] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-11 14:00:45] ## remove_type: ScientificName
[INFO] [2020-06-11 14:00:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:00:45] [14:00:45.476] Removed 0 Scientificnames
[INFO] [2020-06-11 14:00:45] ## remove_type: Vernacular
[INFO] [2020-06-11 14:00:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:00:45] [14:00:45.479] Removed 0 Vernaculars
[INFO] [2020-06-11 14:00:45] ## remove_type: Article
[INFO] [2020-06-11 14:00:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:00:45] [14:00:45.481] Removed 0 Articles
[INFO] [2020-06-11 14:00:45] ## remove_type: Medium
[INFO] [2020-06-11 14:00:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:00:45] [14:00:45.485] Removed 0 Media
[INFO] [2020-06-11 14:00:45] ## remove_type: Trait
[INFO] [2020-06-11 14:00:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:00:45] [14:00:45.488] Removed 0 Traits
[INFO] [2020-06-11 14:00:45] ## remove_type: MetaTrait
[INFO] [2020-06-11 14:00:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:00:45] [14:00:45.490] Removed 0 Metatraits
[INFO] [2020-06-11 14:00:45] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-11 14:00:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:00:45] [14:00:45.493] Removed 0 Occurrencemetadata
[INFO] [2020-06-11 14:00:45] ## remove_type: Assoc
[INFO] [2020-06-11 14:00:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:00:45] [14:00:45.495] Removed 0 Assocs
[INFO] [2020-06-11 14:00:45] ## remove_type: MetaAssoc
[INFO] [2020-06-11 14:00:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:00:45] [14:00:45.498] Removed 0 Metaassocs
[INFO] [2020-06-11 14:00:45] ## remove_type: Identifier
[INFO] [2020-06-11 14:00:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:00:45] [14:00:45.500] Removed 0 Identifiers
[INFO] [2020-06-11 14:00:45] ## remove_type: Reference
[INFO] [2020-06-11 14:00:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:00:45] [14:00:45.503] Removed 0 References
[INFO] [2020-06-11 14:00:45] ## remove_type: Node
[INFO] [2020-06-11 14:00:45] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:00:45] [14:00:45.525] Removed 0 Nodes
[START] [2020-06-11 14:00:45] logged process
[START] [2020-06-11 14:00:45] Creating resource from OpenData
[START] [2020-06-11 14:00:45] logged process
[START] [2020-06-11 14:00:45] Parse meta.xml file and create formats with fields
[STOP] [2020-06-11 14:00:45] Parse meta.xml file and create formats with fields
[STOP] [2020-06-11 14:00:45] Creating resource from OpenData
[START] [2020-06-11 14:00:45] logged process
[START] [2020-06-11 14:00:45] create_harvest_instance
[STOP] [2020-06-11 14:00:46] create_harvest_instance
[START] [2020-06-11 14:00:46] fetch_files
[STOP] [2020-06-11 14:00:46] fetch_files
[START] [2020-06-11 14:00:46] validate_each_file
[STOP] [2020-06-11 14:00:47] validate_each_file
[START] [2020-06-11 14:00:47] convert_to_csv
[CMD] [2020-06-11 14:00:47] /usr/bin/sort /app/public/converted_csv/trova_et_al_trov_nodes_21198.csv > /app/public/converted_csv/trova_et_al_trov_nodes_21198.csv_sorted
[CMD] [2020-06-11 14:00:47] /usr/bin/sort /app/public/converted_csv/trova_et_al_trov_occurrences_21199.csv > /app/public/converted_csv/trova_et_al_trov_occurrences_21199.csv_sorted
[CMD] [2020-06-11 14:00:47] /usr/bin/sort /app/public/converted_csv/trova_et_al_trov_measurements_21200.csv > /app/public/converted_csv/trova_et_al_trov_measurements_21200.csv_sorted
[STOP] [2020-06-11 14:00:47] convert_to_csv
[START] [2020-06-11 14:00:47] calculate_delta
[CMD] [2020-06-11 14:00:47] echo "0a" > /app/public/diff/trova_et_al_trov_nodes_21198.diff
[CMD] [2020-06-11 14:00:47] tail -n +1 /app/public/converted_csv/trova_et_al_trov_nodes_21198.csv >> /app/public/diff/trova_et_al_trov_nodes_21198.diff
[CMD] [2020-06-11 14:00:47] echo "." >> /app/public/diff/trova_et_al_trov_nodes_21198.diff
[CMD] [2020-06-11 14:00:47] echo "0a" > /app/public/diff/trova_et_al_trov_occurrences_21199.diff
[CMD] [2020-06-11 14:00:47] tail -n +1 /app/public/converted_csv/trova_et_al_trov_occurrences_21199.csv >> /app/public/diff/trova_et_al_trov_occurrences_21199.diff
[CMD] [2020-06-11 14:00:47] echo "." >> /app/public/diff/trova_et_al_trov_occurrences_21199.diff
[CMD] [2020-06-11 14:00:47] echo "0a" > /app/public/diff/trova_et_al_trov_measurements_21200.diff
[CMD] [2020-06-11 14:00:47] tail -n +1 /app/public/converted_csv/trova_et_al_trov_measurements_21200.csv >> /app/public/diff/trova_et_al_trov_measurements_21200.diff
[CMD] [2020-06-11 14:00:47] echo "." >> /app/public/diff/trova_et_al_trov_measurements_21200.diff
[STOP] [2020-06-11 14:00:47] calculate_delta
[START] [2020-06-11 14:00:47] parse_diff_and_store
[INFO] [2020-06-11 14:00:47] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-11 14:00:47] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-11 14:00:47] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-11 14:00:47] Storing 5 ScientificNames
[INFO] [2020-06-11 14:00:47] Processing group of 5 in 1 groups of 1000
[INFO] [2020-06-11 14:00:47] Average Time: 0.0
[INFO] [2020-06-11 14:00:47] Total Time: 1s
[INFO] [2020-06-11 14:00:47] Storing 5 Nodes
[INFO] [2020-06-11 14:00:47] Processing group of 5 in 1 groups of 1000
[INFO] [2020-06-11 14:00:47] Average Time: 0.0
[INFO] [2020-06-11 14:00:47] Total Time: 1s
[INFO] [2020-06-11 14:00:47] Storing 2 Occurrences
[INFO] [2020-06-11 14:00:47] Processing group of 2 in 1 groups of 1000
[INFO] [2020-06-11 14:00:47] Average Time: 0.0
[INFO] [2020-06-11 14:00:47] Total Time: 1s
[INFO] [2020-06-11 14:00:47] Storing 4 Traits
[INFO] [2020-06-11 14:00:47] Processing group of 4 in 1 groups of 1000
[INFO] [2020-06-11 14:00:47] Average Time: 0.0
[INFO] [2020-06-11 14:00:47] Total Time: 1s
[INFO] [2020-06-11 14:00:47] Storing 6 MetaTraits
[INFO] [2020-06-11 14:00:47] Processing group of 6 in 1 groups of 1000
[INFO] [2020-06-11 14:00:47] Average Time: 0.0
[INFO] [2020-06-11 14:00:47] Total Time: 1s
[STOP] [2020-06-11 14:00:47] parse_diff_and_store
[START] [2020-06-11 14:00:47] resolve_keys
[INFO] [2020-06-11 14:00:54] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-11 14:00:54] traits to occurrences...
[INFO] [2020-06-11 14:00:54] traits to nodes (through occurrences)...
[INFO] [2020-06-11 14:00:54] Traits to sex term...
[INFO] [2020-06-11 14:00:54] Traits to lifestage term...
[INFO] [2020-06-11 14:00:54] MetaTraits to traits...
[INFO] [2020-06-11 14:00:54] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-11 14:00:54] Assocs to occurrences...
[INFO] [2020-06-11 14:00:54] Assocs to nodes...
[INFO] [2020-06-11 14:00:54] Assoc to sex term...
[INFO] [2020-06-11 14:00:54] Assoc to lifestage term...
[STOP] [2020-06-11 14:00:54] resolve_keys
[START] [2020-06-11 14:00:54] hold_for_later_1
[STOP] [2020-06-11 14:00:54] hold_for_later_1
[START] [2020-06-11 14:00:54] hold_for_later_2
[STOP] [2020-06-11 14:00:54] hold_for_later_2
[START] [2020-06-11 14:00:54] resolve_missing_parents
[STOP] [2020-06-11 14:00:54] resolve_missing_parents
[START] [2020-06-11 14:00:54] rebuild_nodes
[START] [2020-06-11 14:00:54] Flattener#flatten
[START] [2020-06-11 14:00:54] Flattener#study_resource
[START] [2020-06-11 14:00:54] Flattener#build_ancestry
[STOP] [2020-06-11 14:00:54] Flattener#build_ancestry
[INFO] [2020-06-11 14:00:54] 5 ancestry keys
[START] [2020-06-11 14:00:54] build_node_ancestors
[INFO] [2020-06-11 14:00:54] old ancestors deleted.
[STOP] [2020-06-11 14:00:54] build_node_ancestors
[START] [2020-06-11 14:00:54] Flattener#propagate_ancestor_ids
[STOP] [2020-06-11 14:00:54] Flattener#propagate_ancestor_ids
[STOP] [2020-06-11 14:00:54] Flattener#flatten
[STOP] [2020-06-11 14:00:54] rebuild_nodes
[START] [2020-06-11 14:00:54] resolve_missing_media_owners
[STOP] [2020-06-11 14:00:54] resolve_missing_media_owners
[START] [2020-06-11 14:00:54] sanitize_media_verbatims
[STOP] [2020-06-11 14:00:54] sanitize_media_verbatims
[START] [2020-06-11 14:00:54] queue_downloads
[STOP] [2020-06-11 14:00:54] queue_downloads
[START] [2020-06-11 14:00:54] parse_names
[WARN] [2020-06-11 14:00:54] I see 5 names which still need to be parsed.
[STOP] [2020-06-11 14:00:55] parse_names
[START] [2020-06-11 14:00:55] denormalize_canonical_names_to_nodes
[STOP] [2020-06-11 14:00:55] denormalize_canonical_names_to_nodes
[START] [2020-06-11 14:00:55] match_nodes
[START] [2020-06-11 14:00:55] map_all_nodes_to_pages
[STOP] [2020-06-11 14:00:55] map_all_nodes_to_pages
[INFO] [2020-06-11 14:00:55] Unmatched nodes (1 of 5): Citrus sinensis (#80059744)
[START] [2020-06-11 14:00:55] update_nodes
[STOP] [2020-06-11 14:00:55] update_nodes
[STOP] [2020-06-11 14:00:55] match_nodes
[START] [2020-06-11 14:00:55] reindex_search
[STOP] [2020-06-11 14:00:55] reindex_search
[START] [2020-06-11 14:00:55] normalize_units
[STOP] [2020-06-11 14:00:55] normalize_units
[START] [2020-06-11 14:00:55] calculate_statistics
[STOP] [2020-06-11 14:00:55] calculate_statistics
[START] [2020-06-11 14:00:55] complete_harvest_instance
[START] [2020-06-11 14:00:55] overall_tsv_creation
[INFO] [2020-06-11 14:00:55] Processing group of 5 in 1 batches of 10000
[INFO] [2020-06-11 14:01:46] 2 Traits (unfiltered)...
[INFO] [2020-06-11 14:01:59] 2 Traits (filtered)...
[INFO] [2020-06-11 14:01:59] 0 Associations (filtered)...
[INFO] [2020-06-11 14:02:37] 8 metadata added.
[INFO] [2020-06-11 14:02:37] 0 metadata added.
[INFO] [2020-06-11 14:02:37] Average Time: 72.74
[INFO] [2020-06-11 14:02:37] Total Time: 1m42s
[STOP] [2020-06-11 14:02:37] overall_tsv_creation
[INFO] [2020-06-11 14:02:37] Done. Check your files:
[INFO] [2020-06-11 14:02:37] (5 lines) /app/public/data/trova_et_al_trov/publish_nodes.tsv
[INFO] [2020-06-11 14:02:37] (9 lines) /app/public/data/trova_et_al_trov/publish_node_ancestors.tsv
[INFO] [2020-06-11 14:02:37] (5 lines) /app/public/data/trova_et_al_trov/publish_scientific_names.tsv
[INFO] [2020-06-11 14:02:37] (3 lines) /app/public/data/trova_et_al_trov/publish_traits.tsv
[INFO] [2020-06-11 14:02:37] (9 lines) /app/public/data/trova_et_al_trov/publish_metadata.tsv
[STOP] [2020-06-11 14:02:37] complete_harvest_instance
[START] [2020-06-11 14:02:37] completed
[STOP] [2020-06-11 14:02:37] completed
[STOP] [2020-06-11 14:02:37] logged process, took 111.45
[INFO] [2020-06-11 14:05:56] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-11 14:05:57] ## remove_type: ScientificName
[INFO] [2020-06-11 14:05:57] ++ Calling delete_all on 5 instances...
[INFO] [2020-06-11 14:05:57] [14:05:57.871] Removed 5 Scientificnames
[INFO] [2020-06-11 14:05:57] ## remove_type: Vernacular
[INFO] [2020-06-11 14:05:57] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:05:57] [14:05:57.873] Removed 0 Vernaculars
[INFO] [2020-06-11 14:05:57] ## remove_type: Article
[INFO] [2020-06-11 14:05:57] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:05:57] [14:05:57.877] Removed 0 Articles
[INFO] [2020-06-11 14:05:57] ## remove_type: Medium
[INFO] [2020-06-11 14:05:57] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:05:57] [14:05:57.880] Removed 0 Media
[INFO] [2020-06-11 14:05:57] ## remove_type: Trait
[INFO] [2020-06-11 14:05:57] ++ Calling delete_all on 4 instances...
[INFO] [2020-06-11 14:05:57] [14:05:57.884] Removed 4 Traits
[INFO] [2020-06-11 14:05:57] ## remove_type: MetaTrait
[INFO] [2020-06-11 14:05:57] ++ Calling delete_all on 6 instances...
[INFO] [2020-06-11 14:05:57] [14:05:57.888] Removed 6 Metatraits
[INFO] [2020-06-11 14:05:57] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-11 14:05:57] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:05:57] [14:05:57.890] Removed 0 Occurrencemetadata
[INFO] [2020-06-11 14:05:57] ## remove_type: Assoc
[INFO] [2020-06-11 14:05:57] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:05:57] [14:05:57.892] Removed 0 Assocs
[INFO] [2020-06-11 14:05:57] ## remove_type: MetaAssoc
[INFO] [2020-06-11 14:05:57] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:05:57] [14:05:57.895] Removed 0 Metaassocs
[INFO] [2020-06-11 14:05:57] ## remove_type: Identifier
[INFO] [2020-06-11 14:05:57] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:05:57] [14:05:57.897] Removed 0 Identifiers
[INFO] [2020-06-11 14:05:57] ## remove_type: Reference
[INFO] [2020-06-11 14:05:57] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 14:05:57] [14:05:57.899] Removed 0 References
[INFO] [2020-06-11 14:05:57] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:57] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:57] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:57] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:57] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:57] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:57] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:57] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:57] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] Starting batch with ID 80059743...
[INFO] [2020-06-11 14:05:58] ## remove_type: Node
[INFO] [2020-06-11 14:05:58] ++ Calling delete_all on 5 instances...
[INFO] [2020-06-11 14:05:58] [14:05:58.577] Removed 5 Nodes
[START] [2020-06-11 14:05:58] logged process
[START] [2020-06-11 14:05:58] Creating resource from OpenData
[START] [2020-06-11 14:05:59] logged process
[START] [2020-06-11 14:05:59] Parse meta.xml file and create formats with fields
[STOP] [2020-06-11 14:05:59] Parse meta.xml file and create formats with fields
[STOP] [2020-06-11 14:05:59] Creating resource from OpenData
[START] [2020-06-11 14:05:59] logged process
[START] [2020-06-11 14:05:59] create_harvest_instance
[STOP] [2020-06-11 14:06:00] create_harvest_instance
[START] [2020-06-11 14:06:00] fetch_files
[STOP] [2020-06-11 14:06:00] fetch_files
[START] [2020-06-11 14:06:00] validate_each_file
[STOP] [2020-06-11 14:06:00] validate_each_file
[START] [2020-06-11 14:06:00] convert_to_csv
[CMD] [2020-06-11 14:06:00] /usr/bin/sort /app/public/converted_csv/trova_et_al_trov_nodes_21204.csv > /app/public/converted_csv/trova_et_al_trov_nodes_21204.csv_sorted
[CMD] [2020-06-11 14:06:00] /usr/bin/sort /app/public/converted_csv/trova_et_al_trov_occurrences_21205.csv > /app/public/converted_csv/trova_et_al_trov_occurrences_21205.csv_sorted
[CMD] [2020-06-11 14:06:00] /usr/bin/sort /app/public/converted_csv/trova_et_al_trov_measurements_21206.csv > /app/public/converted_csv/trova_et_al_trov_measurements_21206.csv_sorted
[STOP] [2020-06-11 14:06:00] convert_to_csv
[START] [2020-06-11 14:06:00] calculate_delta
[CMD] [2020-06-11 14:06:00] echo "0a" > /app/public/diff/trova_et_al_trov_nodes_21204.diff
[CMD] [2020-06-11 14:06:00] tail -n +1 /app/public/converted_csv/trova_et_al_trov_nodes_21204.csv >> /app/public/diff/trova_et_al_trov_nodes_21204.diff
[CMD] [2020-06-11 14:06:00] echo "." >> /app/public/diff/trova_et_al_trov_nodes_21204.diff
[CMD] [2020-06-11 14:06:00] echo "0a" > /app/public/diff/trova_et_al_trov_occurrences_21205.diff
[CMD] [2020-06-11 14:06:00] tail -n +1 /app/public/converted_csv/trova_et_al_trov_occurrences_21205.csv >> /app/public/diff/trova_et_al_trov_occurrences_21205.diff
[CMD] [2020-06-11 14:06:00] echo "." >> /app/public/diff/trova_et_al_trov_occurrences_21205.diff
[CMD] [2020-06-11 14:06:00] echo "0a" > /app/public/diff/trova_et_al_trov_measurements_21206.diff
[CMD] [2020-06-11 14:06:00] tail -n +1 /app/public/converted_csv/trova_et_al_trov_measurements_21206.csv >> /app/public/diff/trova_et_al_trov_measurements_21206.diff
[CMD] [2020-06-11 14:06:00] echo "." >> /app/public/diff/trova_et_al_trov_measurements_21206.diff
[STOP] [2020-06-11 14:06:00] calculate_delta
[START] [2020-06-11 14:06:00] parse_diff_and_store
[INFO] [2020-06-11 14:06:00] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-11 14:06:00] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-11 14:06:00] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-11 14:06:00] Storing 5 ScientificNames
[INFO] [2020-06-11 14:06:00] Processing group of 5 in 1 groups of 1000
[INFO] [2020-06-11 14:06:00] Average Time: 0.0
[INFO] [2020-06-11 14:06:00] Total Time: 1s
[INFO] [2020-06-11 14:06:00] Storing 5 Nodes
[INFO] [2020-06-11 14:06:00] Processing group of 5 in 1 groups of 1000
[INFO] [2020-06-11 14:06:00] Average Time: 0.0
[INFO] [2020-06-11 14:06:00] Total Time: 1s
[INFO] [2020-06-11 14:06:00] Storing 2 Occurrences
[INFO] [2020-06-11 14:06:00] Processing group of 2 in 1 groups of 1000
[INFO] [2020-06-11 14:06:00] Average Time: 0.0
[INFO] [2020-06-11 14:06:00] Total Time: 1s
[INFO] [2020-06-11 14:06:00] Storing 4 Traits
[INFO] [2020-06-11 14:06:00] Processing group of 4 in 1 groups of 1000
[INFO] [2020-06-11 14:06:00] Average Time: 0.0
[INFO] [2020-06-11 14:06:00] Total Time: 1s
[INFO] [2020-06-11 14:06:00] Storing 6 MetaTraits
[INFO] [2020-06-11 14:06:00] Processing group of 6 in 1 groups of 1000
[INFO] [2020-06-11 14:06:00] Average Time: 0.0
[INFO] [2020-06-11 14:06:00] Total Time: 1s
[STOP] [2020-06-11 14:06:00] parse_diff_and_store
[START] [2020-06-11 14:06:00] resolve_keys
[INFO] [2020-06-11 14:06:07] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-11 14:06:07] traits to occurrences...
[INFO] [2020-06-11 14:06:07] traits to nodes (through occurrences)...
[INFO] [2020-06-11 14:06:07] Traits to sex term...
[INFO] [2020-06-11 14:06:07] Traits to lifestage term...
[INFO] [2020-06-11 14:06:07] MetaTraits to traits...
[INFO] [2020-06-11 14:06:08] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-11 14:06:08] Assocs to occurrences...
[INFO] [2020-06-11 14:06:08] Assocs to nodes...
[INFO] [2020-06-11 14:06:08] Assoc to sex term...
[INFO] [2020-06-11 14:06:08] Assoc to lifestage term...
[STOP] [2020-06-11 14:06:08] resolve_keys
[START] [2020-06-11 14:06:08] hold_for_later_1
[STOP] [2020-06-11 14:06:08] hold_for_later_1
[START] [2020-06-11 14:06:08] hold_for_later_2
[STOP] [2020-06-11 14:06:08] hold_for_later_2
[START] [2020-06-11 14:06:08] resolve_missing_parents
[STOP] [2020-06-11 14:06:08] resolve_missing_parents
[START] [2020-06-11 14:06:08] rebuild_nodes
[START] [2020-06-11 14:06:08] Flattener#flatten
[START] [2020-06-11 14:06:08] Flattener#study_resource
[START] [2020-06-11 14:06:08] Flattener#build_ancestry
[STOP] [2020-06-11 14:06:08] Flattener#build_ancestry
[INFO] [2020-06-11 14:06:08] 5 ancestry keys
[START] [2020-06-11 14:06:08] build_node_ancestors
[INFO] [2020-06-11 14:06:08] old ancestors deleted.
[STOP] [2020-06-11 14:06:08] build_node_ancestors
[START] [2020-06-11 14:06:08] Flattener#propagate_ancestor_ids
[STOP] [2020-06-11 14:06:08] Flattener#propagate_ancestor_ids
[STOP] [2020-06-11 14:06:08] Flattener#flatten
[STOP] [2020-06-11 14:06:08] rebuild_nodes
[START] [2020-06-11 14:06:08] resolve_missing_media_owners
[STOP] [2020-06-11 14:06:08] resolve_missing_media_owners
[START] [2020-06-11 14:06:08] sanitize_media_verbatims
[STOP] [2020-06-11 14:06:08] sanitize_media_verbatims
[START] [2020-06-11 14:06:08] queue_downloads
[STOP] [2020-06-11 14:06:08] queue_downloads
[START] [2020-06-11 14:06:08] parse_names
[WARN] [2020-06-11 14:06:08] I see 5 names which still need to be parsed.
[STOP] [2020-06-11 14:06:09] parse_names
[START] [2020-06-11 14:06:09] denormalize_canonical_names_to_nodes
[STOP] [2020-06-11 14:06:09] denormalize_canonical_names_to_nodes
[START] [2020-06-11 14:06:09] match_nodes
[START] [2020-06-11 14:06:09] map_all_nodes_to_pages
[STOP] [2020-06-11 14:06:09] map_all_nodes_to_pages
[INFO] [2020-06-11 14:06:09] ZERO unmatched nodes (of 5)! Nicely done.
[START] [2020-06-11 14:06:09] update_nodes
[STOP] [2020-06-11 14:06:09] update_nodes
[STOP] [2020-06-11 14:06:09] match_nodes
[START] [2020-06-11 14:06:09] reindex_search
[STOP] [2020-06-11 14:06:09] reindex_search
[START] [2020-06-11 14:06:09] normalize_units
[STOP] [2020-06-11 14:06:09] normalize_units
[START] [2020-06-11 14:06:09] calculate_statistics
[STOP] [2020-06-11 14:06:09] calculate_statistics
[START] [2020-06-11 14:06:09] complete_harvest_instance
[START] [2020-06-11 14:06:09] overall_tsv_creation
[INFO] [2020-06-11 14:06:09] Processing group of 5 in 1 batches of 10000
[INFO] [2020-06-11 14:06:59] 2 Traits (unfiltered)...
[INFO] [2020-06-11 14:07:12] 2 Traits (filtered)...
[INFO] [2020-06-11 14:07:12] 0 Associations (filtered)...
[INFO] [2020-06-11 14:07:48] 8 metadata added.
[INFO] [2020-06-11 14:07:48] 0 metadata added.
[INFO] [2020-06-11 14:07:48] Average Time: 71.52
[INFO] [2020-06-11 14:07:48] Total Time: 1m40s
[STOP] [2020-06-11 14:07:48] overall_tsv_creation
[INFO] [2020-06-11 14:07:48] Done. Check your files:
[INFO] [2020-06-11 14:07:48] (5 lines) /app/public/data/trova_et_al_trov/publish_nodes.tsv
[INFO] [2020-06-11 14:07:48] (9 lines) /app/public/data/trova_et_al_trov/publish_node_ancestors.tsv
[INFO] [2020-06-11 14:07:48] (5 lines) /app/public/data/trova_et_al_trov/publish_scientific_names.tsv
[INFO] [2020-06-11 14:07:48] (3 lines) /app/public/data/trova_et_al_trov/publish_traits.tsv
[INFO] [2020-06-11 14:07:48] (9 lines) /app/public/data/trova_et_al_trov/publish_metadata.tsv
[STOP] [2020-06-11 14:07:48] complete_harvest_instance
[START] [2020-06-11 14:07:48] completed
[STOP] [2020-06-11 14:07:48] completed
[STOP] [2020-06-11 14:07:48] logged process, took 109.51

Latest Process

11 Jun 14:05 EXITED currently processing 0