Harvest for Garland and Losos 1994 Created 22 Jul 15:18

Stage: completed
Fetched: 22 Jul 15:18
Validated: 22 Jul 15:18
Deltas Created 22 Jul 15:18
Units Normalized: 22 Jul 15:18
Ancestry Built: 22 Jul 15:18
Nodes Matched: 22 Jul 15:18
Names Parsed: 22 Jul 15:18
New Models Stored: 22 Jul 15:18
Indexed: 22 Jul 15:18
Completed: 22 Jul 15:19
Time to Harvest: less than a minute
Harvesting Log

(132 lines)
# Logfile created on 2020-07-22 15:13:03 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 15:13:03] logged process
[START] [2020-07-22 15:13:03] Creating resource from OpenData
[START] [2020-07-22 15:13:03] logged process
[START] [2020-07-22 15:13:03] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:13:03] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:13:03] Creating resource from OpenData
[INFO] [2020-07-22 15:17:57] ## HARVEST: type = -harvest
[START] [2020-07-22 15:18:00] logged process
[START] [2020-07-22 15:18:00] create_harvest_instance
[STOP] [2020-07-22 15:18:01] create_harvest_instance
[START] [2020-07-22 15:18:01] fetch_files
[STOP] [2020-07-22 15:18:01] fetch_files
[START] [2020-07-22 15:18:01] validate_each_file
[STOP] [2020-07-22 15:18:01] validate_each_file
[START] [2020-07-22 15:18:01] convert_to_csv
[CMD] [2020-07-22 15:18:01] /usr/bin/sort /app/public/converted_csv/garland_losos_ga_nodes_22066.csv > /app/public/converted_csv/garland_losos_ga_nodes_22066.csv_sorted
[CMD] [2020-07-22 15:18:01] /usr/bin/sort /app/public/converted_csv/garland_losos_ga_occurrences_22067.csv > /app/public/converted_csv/garland_losos_ga_occurrences_22067.csv_sorted
[CMD] [2020-07-22 15:18:01] /usr/bin/sort /app/public/converted_csv/garland_losos_ga_measurements_22068.csv > /app/public/converted_csv/garland_losos_ga_measurements_22068.csv_sorted
[STOP] [2020-07-22 15:18:01] convert_to_csv
[START] [2020-07-22 15:18:01] calculate_delta
[CMD] [2020-07-22 15:18:01] echo "0a" > /app/public/diff/garland_losos_ga_nodes_22066.diff
[CMD] [2020-07-22 15:18:01] tail -n +1 /app/public/converted_csv/garland_losos_ga_nodes_22066.csv >> /app/public/diff/garland_losos_ga_nodes_22066.diff
[CMD] [2020-07-22 15:18:01] echo "." >> /app/public/diff/garland_losos_ga_nodes_22066.diff
[CMD] [2020-07-22 15:18:01] echo "0a" > /app/public/diff/garland_losos_ga_occurrences_22067.diff
[CMD] [2020-07-22 15:18:01] tail -n +1 /app/public/converted_csv/garland_losos_ga_occurrences_22067.csv >> /app/public/diff/garland_losos_ga_occurrences_22067.diff
[CMD] [2020-07-22 15:18:01] echo "." >> /app/public/diff/garland_losos_ga_occurrences_22067.diff
[CMD] [2020-07-22 15:18:01] echo "0a" > /app/public/diff/garland_losos_ga_measurements_22068.diff
[CMD] [2020-07-22 15:18:01] tail -n +1 /app/public/converted_csv/garland_losos_ga_measurements_22068.csv >> /app/public/diff/garland_losos_ga_measurements_22068.diff
[CMD] [2020-07-22 15:18:01] echo "." >> /app/public/diff/garland_losos_ga_measurements_22068.diff
[STOP] [2020-07-22 15:18:01] calculate_delta
[START] [2020-07-22 15:18:01] parse_diff_and_store
[INFO] [2020-07-22 15:18:02] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 15:18:02] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 15:18:02] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 15:18:02] Storing 5 ScientificNames
[INFO] [2020-07-22 15:18:02] Processing group of 5 in 1 groups of 1000
[INFO] [2020-07-22 15:18:02] Average Time: 0.01
[INFO] [2020-07-22 15:18:02] Total Time: 1s
[INFO] [2020-07-22 15:18:02] Storing 5 Nodes
[INFO] [2020-07-22 15:18:02] Processing group of 5 in 1 groups of 1000
[INFO] [2020-07-22 15:18:02] Average Time: 0.0
[INFO] [2020-07-22 15:18:02] Total Time: 1s
[INFO] [2020-07-22 15:18:02] Storing 5 Occurrences
[INFO] [2020-07-22 15:18:02] Processing group of 5 in 1 groups of 1000
[INFO] [2020-07-22 15:18:02] Average Time: 0.0
[INFO] [2020-07-22 15:18:02] Total Time: 1s
[INFO] [2020-07-22 15:18:02] Storing 9 Traits
[INFO] [2020-07-22 15:18:02] Processing group of 9 in 1 groups of 1000
[INFO] [2020-07-22 15:18:02] Average Time: 0.0
[INFO] [2020-07-22 15:18:02] Total Time: 1s
[INFO] [2020-07-22 15:18:02] Storing 10 MetaTraits
[INFO] [2020-07-22 15:18:02] Processing group of 10 in 1 groups of 1000
[INFO] [2020-07-22 15:18:02] Average Time: 0.0
[INFO] [2020-07-22 15:18:02] Total Time: 1s
[STOP] [2020-07-22 15:18:02] parse_diff_and_store
[START] [2020-07-22 15:18:02] resolve_keys
[INFO] [2020-07-22 15:18:09] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 15:18:09] traits to occurrences...
[INFO] [2020-07-22 15:18:09] traits to nodes (through occurrences)...
[INFO] [2020-07-22 15:18:09] Traits to sex term...
[INFO] [2020-07-22 15:18:09] Traits to lifestage term...
[INFO] [2020-07-22 15:18:09] MetaTraits to traits...
[INFO] [2020-07-22 15:18:09] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 15:18:09] Assocs to occurrences...
[INFO] [2020-07-22 15:18:09] Assocs to nodes...
[INFO] [2020-07-22 15:18:09] Assoc to sex term...
[INFO] [2020-07-22 15:18:09] Assoc to lifestage term...
[STOP] [2020-07-22 15:18:09] resolve_keys
[START] [2020-07-22 15:18:09] hold_for_later_1
[STOP] [2020-07-22 15:18:09] hold_for_later_1
[START] [2020-07-22 15:18:09] hold_for_later_2
[STOP] [2020-07-22 15:18:09] hold_for_later_2
[START] [2020-07-22 15:18:09] resolve_missing_parents
[STOP] [2020-07-22 15:18:09] resolve_missing_parents
[START] [2020-07-22 15:18:09] rebuild_nodes
[START] [2020-07-22 15:18:09] Flattener#flatten
[START] [2020-07-22 15:18:09] Flattener#study_resource
[START] [2020-07-22 15:18:09] Flattener#build_ancestry
[STOP] [2020-07-22 15:18:09] Flattener#build_ancestry
[INFO] [2020-07-22 15:18:09] 5 ancestry keys
[START] [2020-07-22 15:18:09] build_node_ancestors
[INFO] [2020-07-22 15:18:09] old ancestors deleted.
[STOP] [2020-07-22 15:18:09] build_node_ancestors
[WARN] [2020-07-22 15:18:09] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 15:18:09] Flattener#flatten
[STOP] [2020-07-22 15:18:09] rebuild_nodes
[START] [2020-07-22 15:18:09] resolve_missing_media_owners
[STOP] [2020-07-22 15:18:09] resolve_missing_media_owners
[START] [2020-07-22 15:18:09] sanitize_media_verbatims
[STOP] [2020-07-22 15:18:09] sanitize_media_verbatims
[START] [2020-07-22 15:18:09] queue_downloads
[STOP] [2020-07-22 15:18:09] queue_downloads
[START] [2020-07-22 15:18:09] parse_names
[WARN] [2020-07-22 15:18:09] I see 5 names which still need to be parsed.
[STOP] [2020-07-22 15:18:10] parse_names
[START] [2020-07-22 15:18:10] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 15:18:10] denormalize_canonical_names_to_nodes
[START] [2020-07-22 15:18:10] match_nodes
[START] [2020-07-22 15:18:10] map_all_nodes_to_pages
[STOP] [2020-07-22 15:18:10] map_all_nodes_to_pages
[INFO] [2020-07-22 15:18:10] ZERO unmatched nodes (of 5)! Nicely done.
[START] [2020-07-22 15:18:10] update_nodes
[STOP] [2020-07-22 15:18:10] update_nodes
[STOP] [2020-07-22 15:18:10] match_nodes
[START] [2020-07-22 15:18:10] reindex_search
[STOP] [2020-07-22 15:18:10] reindex_search
[START] [2020-07-22 15:18:10] normalize_units
[STOP] [2020-07-22 15:18:10] normalize_units
[START] [2020-07-22 15:18:10] calculate_statistics
[2020-07-22 15:18:10] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 15:18:10] calculate_statistics
[START] [2020-07-22 15:18:10] complete_harvest_instance
[START] [2020-07-22 15:18:10] overall_tsv_creation
[INFO] [2020-07-22 15:18:10] Processing group of 5 in 1 batches of 10000
[INFO] [2020-07-22 15:18:58] 5 Traits (unfiltered)...
[INFO] [2020-07-22 15:19:35] 5 Traits (filtered)...
[INFO] [2020-07-22 15:19:35] 0 Associations (filtered)...
[INFO] [2020-07-22 15:19:35] 14 metadata added.
[INFO] [2020-07-22 15:19:35] 0 metadata added.
[INFO] [2020-07-22 15:19:35] Average Time: 57.83
[INFO] [2020-07-22 15:19:35] Total Time: 1m25s
[STOP] [2020-07-22 15:19:35] overall_tsv_creation
[INFO] [2020-07-22 15:19:35] Done. Check your files:
[INFO] [2020-07-22 15:19:35] (5 lines) /app/public/data/garland_losos_ga/publish_nodes.tsv
[INFO] [2020-07-22 15:19:35] (5 lines) /app/public/data/garland_losos_ga/publish_scientific_names.tsv
[INFO] [2020-07-22 15:19:35] (6 lines) /app/public/data/garland_losos_ga/publish_traits.tsv
[INFO] [2020-07-22 15:19:35] (5 lines) /app/public/data/garland_losos_ga/publish_metadata.tsv
[STOP] [2020-07-22 15:19:35] complete_harvest_instance
[START] [2020-07-22 15:19:35] completed
[STOP] [2020-07-22 15:19:35] completed
[STOP] [2020-07-22 15:19:35] logged process, took 94.48
Latest Process

22 Jul 15:18 EXITED currently processing 0