Harvest for Okoli et al 2012 Created 11 Jun 13:57

Stage: completed
Fetched: 11 Jun 13:57
Validated: 11 Jun 13:57
Deltas Created 11 Jun 13:57
Units Normalized: 11 Jun 13:58
Ancestry Built: 11 Jun 13:58
Nodes Matched: 11 Jun 13:58
Names Parsed: 11 Jun 13:58
New Models Stored: 11 Jun 13:57
Indexed: 11 Jun 13:58
Completed: 11 Jun 13:59
Time to Harvest: less than a minute
Harvesting Log

(169 lines)
# Logfile created on 2020-06-11 13:57:50 -0400 by logger.rb/v1.4.2
[INFO] [2020-06-11 13:57:50] ## HARVEST: type = re_download_opendata_-harvest
[INFO] [2020-06-11 13:57:53] ## remove_type: ScientificName
[INFO] [2020-06-11 13:57:53] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:57:53] [13:57:53.284] Removed 0 Scientificnames
[INFO] [2020-06-11 13:57:53] ## remove_type: Vernacular
[INFO] [2020-06-11 13:57:53] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:57:53] [13:57:53.288] Removed 0 Vernaculars
[INFO] [2020-06-11 13:57:53] ## remove_type: Article
[INFO] [2020-06-11 13:57:53] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:57:53] [13:57:53.290] Removed 0 Articles
[INFO] [2020-06-11 13:57:53] ## remove_type: Medium
[INFO] [2020-06-11 13:57:53] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:57:53] [13:57:53.293] Removed 0 Media
[INFO] [2020-06-11 13:57:53] ## remove_type: Trait
[INFO] [2020-06-11 13:57:53] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:57:53] [13:57:53.297] Removed 0 Traits
[INFO] [2020-06-11 13:57:53] ## remove_type: MetaTrait
[INFO] [2020-06-11 13:57:53] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:57:53] [13:57:53.299] Removed 0 Metatraits
[INFO] [2020-06-11 13:57:53] ## remove_type: OccurrenceMetadatum
[INFO] [2020-06-11 13:57:53] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:57:53] [13:57:53.302] Removed 0 Occurrencemetadata
[INFO] [2020-06-11 13:57:53] ## remove_type: Assoc
[INFO] [2020-06-11 13:57:53] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:57:53] [13:57:53.305] Removed 0 Assocs
[INFO] [2020-06-11 13:57:53] ## remove_type: MetaAssoc
[INFO] [2020-06-11 13:57:53] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:57:53] [13:57:53.308] Removed 0 Metaassocs
[INFO] [2020-06-11 13:57:53] ## remove_type: Identifier
[INFO] [2020-06-11 13:57:53] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:57:53] [13:57:53.310] Removed 0 Identifiers
[INFO] [2020-06-11 13:57:53] ## remove_type: Reference
[INFO] [2020-06-11 13:57:53] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:57:53] [13:57:53.313] Removed 0 References
[INFO] [2020-06-11 13:57:53] ## remove_type: Node
[INFO] [2020-06-11 13:57:53] ++ Calling delete_all on 0 instances...
[INFO] [2020-06-11 13:57:53] [13:57:53.333] Removed 0 Nodes
[START] [2020-06-11 13:57:53] logged process
[START] [2020-06-11 13:57:53] Creating resource from OpenData
[START] [2020-06-11 13:57:53] logged process
[START] [2020-06-11 13:57:53] Parse meta.xml file and create formats with fields
[STOP] [2020-06-11 13:57:53] Parse meta.xml file and create formats with fields
[STOP] [2020-06-11 13:57:53] Creating resource from OpenData
[START] [2020-06-11 13:57:53] logged process
[START] [2020-06-11 13:57:53] create_harvest_instance
[STOP] [2020-06-11 13:57:54] create_harvest_instance
[START] [2020-06-11 13:57:54] fetch_files
[STOP] [2020-06-11 13:57:54] fetch_files
[START] [2020-06-11 13:57:54] validate_each_file
[STOP] [2020-06-11 13:57:54] validate_each_file
[START] [2020-06-11 13:57:54] convert_to_csv
[CMD] [2020-06-11 13:57:54] /usr/bin/sort /app/public/converted_csv/okoli_et_al_okol_nodes_21192.csv > /app/public/converted_csv/okoli_et_al_okol_nodes_21192.csv_sorted
[CMD] [2020-06-11 13:57:54] /usr/bin/sort /app/public/converted_csv/okoli_et_al_okol_occurrences_21193.csv > /app/public/converted_csv/okoli_et_al_okol_occurrences_21193.csv_sorted
[CMD] [2020-06-11 13:57:54] /usr/bin/sort /app/public/converted_csv/okoli_et_al_okol_measurements_21194.csv > /app/public/converted_csv/okoli_et_al_okol_measurements_21194.csv_sorted
[STOP] [2020-06-11 13:57:54] convert_to_csv
[START] [2020-06-11 13:57:54] calculate_delta
[CMD] [2020-06-11 13:57:54] echo "0a" > /app/public/diff/okoli_et_al_okol_nodes_21192.diff
[CMD] [2020-06-11 13:57:54] tail -n +1 /app/public/converted_csv/okoli_et_al_okol_nodes_21192.csv >> /app/public/diff/okoli_et_al_okol_nodes_21192.diff
[CMD] [2020-06-11 13:57:54] echo "." >> /app/public/diff/okoli_et_al_okol_nodes_21192.diff
[CMD] [2020-06-11 13:57:54] echo "0a" > /app/public/diff/okoli_et_al_okol_occurrences_21193.diff
[CMD] [2020-06-11 13:57:54] tail -n +1 /app/public/converted_csv/okoli_et_al_okol_occurrences_21193.csv >> /app/public/diff/okoli_et_al_okol_occurrences_21193.diff
[CMD] [2020-06-11 13:57:54] echo "." >> /app/public/diff/okoli_et_al_okol_occurrences_21193.diff
[CMD] [2020-06-11 13:57:54] echo "0a" > /app/public/diff/okoli_et_al_okol_measurements_21194.diff
[CMD] [2020-06-11 13:57:54] tail -n +1 /app/public/converted_csv/okoli_et_al_okol_measurements_21194.csv >> /app/public/diff/okoli_et_al_okol_measurements_21194.diff
[CMD] [2020-06-11 13:57:54] echo "." >> /app/public/diff/okoli_et_al_okol_measurements_21194.diff
[STOP] [2020-06-11 13:57:54] calculate_delta
[START] [2020-06-11 13:57:54] parse_diff_and_store
[INFO] [2020-06-11 13:57:54] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-11 13:57:54] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-11 13:57:54] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-11 13:57:55] Storing 6 ScientificNames
[INFO] [2020-06-11 13:57:55] Processing group of 6 in 1 groups of 1000
[INFO] [2020-06-11 13:57:55] Average Time: 0.01
[INFO] [2020-06-11 13:57:55] Total Time: 1s
[INFO] [2020-06-11 13:57:55] Storing 6 Nodes
[INFO] [2020-06-11 13:57:55] Processing group of 6 in 1 groups of 1000
[INFO] [2020-06-11 13:57:55] Average Time: 0.0
[INFO] [2020-06-11 13:57:55] Total Time: 1s
[INFO] [2020-06-11 13:57:55] Storing 3 Occurrences
[INFO] [2020-06-11 13:57:55] Processing group of 3 in 1 groups of 1000
[INFO] [2020-06-11 13:57:55] Average Time: 0.0
[INFO] [2020-06-11 13:57:55] Total Time: 1s
[INFO] [2020-06-11 13:57:55] Storing 9 Traits
[INFO] [2020-06-11 13:57:55] Processing group of 9 in 1 groups of 1000
[INFO] [2020-06-11 13:57:55] Average Time: 0.0
[INFO] [2020-06-11 13:57:55] Total Time: 1s
[INFO] [2020-06-11 13:57:55] Storing 9 MetaTraits
[INFO] [2020-06-11 13:57:55] Processing group of 9 in 1 groups of 1000
[INFO] [2020-06-11 13:57:55] Average Time: 0.0
[INFO] [2020-06-11 13:57:55] Total Time: 1s
[STOP] [2020-06-11 13:57:55] parse_diff_and_store
[START] [2020-06-11 13:57:55] resolve_keys
[INFO] [2020-06-11 13:58:01] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-11 13:58:01] traits to occurrences...
[INFO] [2020-06-11 13:58:01] traits to nodes (through occurrences)...
[INFO] [2020-06-11 13:58:01] Traits to sex term...
[INFO] [2020-06-11 13:58:01] Traits to lifestage term...
[INFO] [2020-06-11 13:58:01] MetaTraits to traits...
[INFO] [2020-06-11 13:58:01] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-11 13:58:01] Assocs to occurrences...
[INFO] [2020-06-11 13:58:01] Assocs to nodes...
[INFO] [2020-06-11 13:58:01] Assoc to sex term...
[INFO] [2020-06-11 13:58:01] Assoc to lifestage term...
[STOP] [2020-06-11 13:58:01] resolve_keys
[START] [2020-06-11 13:58:01] hold_for_later_1
[STOP] [2020-06-11 13:58:01] hold_for_later_1
[START] [2020-06-11 13:58:01] hold_for_later_2
[STOP] [2020-06-11 13:58:01] hold_for_later_2
[START] [2020-06-11 13:58:01] resolve_missing_parents
[STOP] [2020-06-11 13:58:01] resolve_missing_parents
[START] [2020-06-11 13:58:01] rebuild_nodes
[START] [2020-06-11 13:58:01] Flattener#flatten
[START] [2020-06-11 13:58:01] Flattener#study_resource
[START] [2020-06-11 13:58:01] Flattener#build_ancestry
[STOP] [2020-06-11 13:58:01] Flattener#build_ancestry
[INFO] [2020-06-11 13:58:01] 6 ancestry keys
[START] [2020-06-11 13:58:01] build_node_ancestors
[INFO] [2020-06-11 13:58:01] old ancestors deleted.
[STOP] [2020-06-11 13:58:01] build_node_ancestors
[START] [2020-06-11 13:58:01] Flattener#propagate_ancestor_ids
[STOP] [2020-06-11 13:58:01] Flattener#propagate_ancestor_ids
[STOP] [2020-06-11 13:58:01] Flattener#flatten
[STOP] [2020-06-11 13:58:01] rebuild_nodes
[START] [2020-06-11 13:58:01] resolve_missing_media_owners
[STOP] [2020-06-11 13:58:01] resolve_missing_media_owners
[START] [2020-06-11 13:58:01] sanitize_media_verbatims
[STOP] [2020-06-11 13:58:01] sanitize_media_verbatims
[START] [2020-06-11 13:58:01] queue_downloads
[STOP] [2020-06-11 13:58:02] queue_downloads
[START] [2020-06-11 13:58:02] parse_names
[WARN] [2020-06-11 13:58:02] I see 6 names which still need to be parsed.
[STOP] [2020-06-11 13:58:03] parse_names
[START] [2020-06-11 13:58:03] denormalize_canonical_names_to_nodes
[STOP] [2020-06-11 13:58:03] denormalize_canonical_names_to_nodes
[START] [2020-06-11 13:58:03] match_nodes
[START] [2020-06-11 13:58:03] map_all_nodes_to_pages
[STOP] [2020-06-11 13:58:03] map_all_nodes_to_pages
[INFO] [2020-06-11 13:58:03] Unmatched nodes (1 of 6): Cola garcina (#80059738)
[START] [2020-06-11 13:58:03] update_nodes
[STOP] [2020-06-11 13:58:03] update_nodes
[STOP] [2020-06-11 13:58:03] match_nodes
[START] [2020-06-11 13:58:03] reindex_search
[STOP] [2020-06-11 13:58:03] reindex_search
[START] [2020-06-11 13:58:03] normalize_units
[STOP] [2020-06-11 13:58:03] normalize_units
[START] [2020-06-11 13:58:03] calculate_statistics
[STOP] [2020-06-11 13:58:03] calculate_statistics
[START] [2020-06-11 13:58:03] complete_harvest_instance
[START] [2020-06-11 13:58:03] overall_tsv_creation
[INFO] [2020-06-11 13:58:03] Processing group of 6 in 1 batches of 10000
[INFO] [2020-06-11 13:58:53] 3 Traits (unfiltered)...
[INFO] [2020-06-11 13:59:06] 3 Traits (filtered)...
[INFO] [2020-06-11 13:59:06] 0 Associations (filtered)...
[INFO] [2020-06-11 13:59:43] 12 metadata added.
[INFO] [2020-06-11 13:59:43] 0 metadata added.
[INFO] [2020-06-11 13:59:43] Average Time: 71.78
[INFO] [2020-06-11 13:59:43] Total Time: 1m40s
[STOP] [2020-06-11 13:59:43] overall_tsv_creation
[INFO] [2020-06-11 13:59:43] Done. Check your files:
[INFO] [2020-06-11 13:59:43] (6 lines) /app/public/data/okoli_et_al_okol/publish_nodes.tsv
[INFO] [2020-06-11 13:59:43] (12 lines) /app/public/data/okoli_et_al_okol/publish_node_ancestors.tsv
[INFO] [2020-06-11 13:59:43] (6 lines) /app/public/data/okoli_et_al_okol/publish_scientific_names.tsv
[INFO] [2020-06-11 13:59:43] (4 lines) /app/public/data/okoli_et_al_okol/publish_traits.tsv
[INFO] [2020-06-11 13:59:43] (13 lines) /app/public/data/okoli_et_al_okol/publish_metadata.tsv
[STOP] [2020-06-11 13:59:43] complete_harvest_instance
[START] [2020-06-11 13:59:43] completed
[STOP] [2020-06-11 13:59:43] completed
[STOP] [2020-06-11 13:59:43] logged process, took 109.59
Latest Process

11 Jun 13:57 EXITED currently processing 0