Harvest for Shen 2010 Created 22 Jul 15:15

Stage: completed
Fetched: 22 Jul 15:15
Validated: 22 Jul 15:15
Deltas Created 22 Jul 15:15
Units Normalized: 22 Jul 15:15
Ancestry Built: 22 Jul 15:15
Nodes Matched: 22 Jul 15:15
Names Parsed: 22 Jul 15:15
New Models Stored: 22 Jul 15:15
Indexed: 22 Jul 15:15
Completed: 22 Jul 15:16
Time to Harvest: less than a minute
Harvesting Log

(132 lines)
# Logfile created on 2020-07-22 15:10:42 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 15:10:42] logged process
[START] [2020-07-22 15:10:42] Creating resource from OpenData
[START] [2020-07-22 15:10:42] logged process
[START] [2020-07-22 15:10:42] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:10:42] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:10:42] Creating resource from OpenData
[INFO] [2020-07-22 15:15:18] ## HARVEST: type = -harvest
[START] [2020-07-22 15:15:19] logged process
[START] [2020-07-22 15:15:19] create_harvest_instance
[STOP] [2020-07-22 15:15:20] create_harvest_instance
[START] [2020-07-22 15:15:20] fetch_files
[STOP] [2020-07-22 15:15:20] fetch_files
[START] [2020-07-22 15:15:20] validate_each_file
[STOP] [2020-07-22 15:15:20] validate_each_file
[START] [2020-07-22 15:15:20] convert_to_csv
[CMD] [2020-07-22 15:15:20] /usr/bin/sort /app/public/converted_csv/shen_shen_2010_nodes_22060.csv > /app/public/converted_csv/shen_shen_2010_nodes_22060.csv_sorted
[CMD] [2020-07-22 15:15:20] /usr/bin/sort /app/public/converted_csv/shen_shen_2010_occurrences_22061.csv > /app/public/converted_csv/shen_shen_2010_occurrences_22061.csv_sorted
[CMD] [2020-07-22 15:15:20] /usr/bin/sort /app/public/converted_csv/shen_shen_2010_measurements_22062.csv > /app/public/converted_csv/shen_shen_2010_measurements_22062.csv_sorted
[STOP] [2020-07-22 15:15:20] convert_to_csv
[START] [2020-07-22 15:15:20] calculate_delta
[CMD] [2020-07-22 15:15:20] echo "0a" > /app/public/diff/shen_shen_2010_nodes_22060.diff
[CMD] [2020-07-22 15:15:20] tail -n +1 /app/public/converted_csv/shen_shen_2010_nodes_22060.csv >> /app/public/diff/shen_shen_2010_nodes_22060.diff
[CMD] [2020-07-22 15:15:20] echo "." >> /app/public/diff/shen_shen_2010_nodes_22060.diff
[CMD] [2020-07-22 15:15:20] echo "0a" > /app/public/diff/shen_shen_2010_occurrences_22061.diff
[CMD] [2020-07-22 15:15:20] tail -n +1 /app/public/converted_csv/shen_shen_2010_occurrences_22061.csv >> /app/public/diff/shen_shen_2010_occurrences_22061.diff
[CMD] [2020-07-22 15:15:20] echo "." >> /app/public/diff/shen_shen_2010_occurrences_22061.diff
[CMD] [2020-07-22 15:15:20] echo "0a" > /app/public/diff/shen_shen_2010_measurements_22062.diff
[CMD] [2020-07-22 15:15:20] tail -n +1 /app/public/converted_csv/shen_shen_2010_measurements_22062.csv >> /app/public/diff/shen_shen_2010_measurements_22062.diff
[CMD] [2020-07-22 15:15:20] echo "." >> /app/public/diff/shen_shen_2010_measurements_22062.diff
[STOP] [2020-07-22 15:15:20] calculate_delta
[START] [2020-07-22 15:15:21] parse_diff_and_store
[INFO] [2020-07-22 15:15:21] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 15:15:21] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 15:15:21] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 15:15:21] Storing 1 ScientificNames
[INFO] [2020-07-22 15:15:21] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 15:15:21] Average Time: 0.0
[INFO] [2020-07-22 15:15:21] Total Time: 1s
[INFO] [2020-07-22 15:15:21] Storing 1 Nodes
[INFO] [2020-07-22 15:15:21] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 15:15:21] Average Time: 0.0
[INFO] [2020-07-22 15:15:21] Total Time: 1s
[INFO] [2020-07-22 15:15:21] Storing 1 Occurrences
[INFO] [2020-07-22 15:15:21] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-22 15:15:21] Average Time: 0.0
[INFO] [2020-07-22 15:15:21] Total Time: 1s
[INFO] [2020-07-22 15:15:21] Storing 2 Traits
[INFO] [2020-07-22 15:15:21] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 15:15:21] Average Time: 0.0
[INFO] [2020-07-22 15:15:21] Total Time: 1s
[INFO] [2020-07-22 15:15:21] Storing 2 MetaTraits
[INFO] [2020-07-22 15:15:21] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 15:15:21] Average Time: 0.0
[INFO] [2020-07-22 15:15:21] Total Time: 1s
[STOP] [2020-07-22 15:15:21] parse_diff_and_store
[START] [2020-07-22 15:15:21] resolve_keys
[INFO] [2020-07-22 15:15:28] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 15:15:28] traits to occurrences...
[INFO] [2020-07-22 15:15:28] traits to nodes (through occurrences)...
[INFO] [2020-07-22 15:15:28] Traits to sex term...
[INFO] [2020-07-22 15:15:28] Traits to lifestage term...
[INFO] [2020-07-22 15:15:28] MetaTraits to traits...
[INFO] [2020-07-22 15:15:28] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 15:15:28] Assocs to occurrences...
[INFO] [2020-07-22 15:15:28] Assocs to nodes...
[INFO] [2020-07-22 15:15:28] Assoc to sex term...
[INFO] [2020-07-22 15:15:28] Assoc to lifestage term...
[STOP] [2020-07-22 15:15:28] resolve_keys
[START] [2020-07-22 15:15:28] hold_for_later_1
[STOP] [2020-07-22 15:15:28] hold_for_later_1
[START] [2020-07-22 15:15:28] hold_for_later_2
[STOP] [2020-07-22 15:15:28] hold_for_later_2
[START] [2020-07-22 15:15:28] resolve_missing_parents
[STOP] [2020-07-22 15:15:28] resolve_missing_parents
[START] [2020-07-22 15:15:28] rebuild_nodes
[START] [2020-07-22 15:15:28] Flattener#flatten
[START] [2020-07-22 15:15:28] Flattener#study_resource
[START] [2020-07-22 15:15:28] Flattener#build_ancestry
[STOP] [2020-07-22 15:15:28] Flattener#build_ancestry
[INFO] [2020-07-22 15:15:28] 1 ancestry keys
[START] [2020-07-22 15:15:28] build_node_ancestors
[INFO] [2020-07-22 15:15:28] old ancestors deleted.
[STOP] [2020-07-22 15:15:28] build_node_ancestors
[WARN] [2020-07-22 15:15:28] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 15:15:28] Flattener#flatten
[STOP] [2020-07-22 15:15:28] rebuild_nodes
[START] [2020-07-22 15:15:28] resolve_missing_media_owners
[STOP] [2020-07-22 15:15:28] resolve_missing_media_owners
[START] [2020-07-22 15:15:28] sanitize_media_verbatims
[STOP] [2020-07-22 15:15:28] sanitize_media_verbatims
[START] [2020-07-22 15:15:28] queue_downloads
[STOP] [2020-07-22 15:15:28] queue_downloads
[START] [2020-07-22 15:15:28] parse_names
[WARN] [2020-07-22 15:15:28] I see 1 names which still need to be parsed.
[STOP] [2020-07-22 15:15:29] parse_names
[START] [2020-07-22 15:15:29] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 15:15:29] denormalize_canonical_names_to_nodes
[START] [2020-07-22 15:15:29] match_nodes
[START] [2020-07-22 15:15:29] map_all_nodes_to_pages
[STOP] [2020-07-22 15:15:29] map_all_nodes_to_pages
[INFO] [2020-07-22 15:15:29] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-07-22 15:15:29] update_nodes
[STOP] [2020-07-22 15:15:29] update_nodes
[STOP] [2020-07-22 15:15:29] match_nodes
[START] [2020-07-22 15:15:29] reindex_search
[STOP] [2020-07-22 15:15:29] reindex_search
[START] [2020-07-22 15:15:29] normalize_units
[STOP] [2020-07-22 15:15:29] normalize_units
[START] [2020-07-22 15:15:29] calculate_statistics
[2020-07-22 15:15:29] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 15:15:29] calculate_statistics
[START] [2020-07-22 15:15:29] complete_harvest_instance
[START] [2020-07-22 15:15:29] overall_tsv_creation
[INFO] [2020-07-22 15:15:29] Processing group of 1 in 1 batches of 10000
[INFO] [2020-07-22 15:16:17] 1 Traits (unfiltered)...
[INFO] [2020-07-22 15:16:53] 1 Traits (filtered)...
[INFO] [2020-07-22 15:16:53] 0 Associations (filtered)...
[INFO] [2020-07-22 15:16:53] 3 metadata added.
[INFO] [2020-07-22 15:16:53] 0 metadata added.
[INFO] [2020-07-22 15:16:53] Average Time: 56.55
[INFO] [2020-07-22 15:16:53] Total Time: 1m24s
[STOP] [2020-07-22 15:16:53] overall_tsv_creation
[INFO] [2020-07-22 15:16:53] Done. Check your files:
[INFO] [2020-07-22 15:16:53] (1 lines) /app/public/data/shen_shen_2010/publish_nodes.tsv
[INFO] [2020-07-22 15:16:53] (1 lines) /app/public/data/shen_shen_2010/publish_scientific_names.tsv
[INFO] [2020-07-22 15:16:53] (2 lines) /app/public/data/shen_shen_2010/publish_traits.tsv
[INFO] [2020-07-22 15:16:53] (2 lines) /app/public/data/shen_shen_2010/publish_metadata.tsv
[STOP] [2020-07-22 15:16:53] complete_harvest_instance
[START] [2020-07-22 15:16:53] completed
[STOP] [2020-07-22 15:16:53] completed
[STOP] [2020-07-22 15:16:53] logged process, took 93.31
Latest Process

22 Jul 15:15 EXITED currently processing 0