Harvest for Buskey et al 2012 Created 30 Jul 15:07

Stage: completed
Fetched: 30 Jul 15:07
Validated: 30 Jul 15:07
Deltas Created 30 Jul 15:07
Units Normalized: 30 Jul 15:07
Ancestry Built: 30 Jul 15:07
Nodes Matched: 30 Jul 15:07
Names Parsed: 30 Jul 15:07
New Models Stored: 30 Jul 15:07
Indexed: 30 Jul 15:07
Completed: 30 Jul 15:09
Time to Harvest: less than a minute
Harvesting Log

(141 lines)
# Logfile created on 2020-07-30 15:07:27 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 15:07:27] logged process
[START] [2020-07-30 15:07:27] Creating resource from OpenData
[START] [2020-07-30 15:07:27] logged process
[START] [2020-07-30 15:07:27] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 15:07:27] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 15:07:27] Creating resource from OpenData
[INFO] [2020-07-30 15:07:43] ## HARVEST: type = -harvest
[START] [2020-07-30 15:07:48] logged process
[START] [2020-07-30 15:07:48] create_harvest_instance
[STOP] [2020-07-30 15:07:50] create_harvest_instance
[START] [2020-07-30 15:07:50] fetch_files
[STOP] [2020-07-30 15:07:50] fetch_files
[START] [2020-07-30 15:07:50] validate_each_file
[STOP] [2020-07-30 15:07:50] validate_each_file
[START] [2020-07-30 15:07:50] convert_to_csv
[CMD] [2020-07-30 15:07:50] /usr/bin/sort /app/public/converted_csv/buskey_et_al_bus_refs_22368.csv > /app/public/converted_csv/buskey_et_al_bus_refs_22368.csv_sorted
[CMD] [2020-07-30 15:07:50] /usr/bin/sort /app/public/converted_csv/buskey_et_al_bus_nodes_22369.csv > /app/public/converted_csv/buskey_et_al_bus_nodes_22369.csv_sorted
[CMD] [2020-07-30 15:07:50] /usr/bin/sort /app/public/converted_csv/buskey_et_al_bus_occurrences_22370.csv > /app/public/converted_csv/buskey_et_al_bus_occurrences_22370.csv_sorted
[CMD] [2020-07-30 15:07:50] /usr/bin/sort /app/public/converted_csv/buskey_et_al_bus_measurements_22371.csv > /app/public/converted_csv/buskey_et_al_bus_measurements_22371.csv_sorted
[STOP] [2020-07-30 15:07:50] convert_to_csv
[START] [2020-07-30 15:07:50] calculate_delta
[CMD] [2020-07-30 15:07:50] echo "0a" > /app/public/diff/buskey_et_al_bus_refs_22368.diff
[CMD] [2020-07-30 15:07:50] tail -n +1 /app/public/converted_csv/buskey_et_al_bus_refs_22368.csv >> /app/public/diff/buskey_et_al_bus_refs_22368.diff
[CMD] [2020-07-30 15:07:50] echo "." >> /app/public/diff/buskey_et_al_bus_refs_22368.diff
[CMD] [2020-07-30 15:07:50] echo "0a" > /app/public/diff/buskey_et_al_bus_nodes_22369.diff
[CMD] [2020-07-30 15:07:50] tail -n +1 /app/public/converted_csv/buskey_et_al_bus_nodes_22369.csv >> /app/public/diff/buskey_et_al_bus_nodes_22369.diff
[CMD] [2020-07-30 15:07:50] echo "." >> /app/public/diff/buskey_et_al_bus_nodes_22369.diff
[CMD] [2020-07-30 15:07:50] echo "0a" > /app/public/diff/buskey_et_al_bus_occurrences_22370.diff
[CMD] [2020-07-30 15:07:50] tail -n +1 /app/public/converted_csv/buskey_et_al_bus_occurrences_22370.csv >> /app/public/diff/buskey_et_al_bus_occurrences_22370.diff
[CMD] [2020-07-30 15:07:50] echo "." >> /app/public/diff/buskey_et_al_bus_occurrences_22370.diff
[CMD] [2020-07-30 15:07:50] echo "0a" > /app/public/diff/buskey_et_al_bus_measurements_22371.diff
[CMD] [2020-07-30 15:07:50] tail -n +1 /app/public/converted_csv/buskey_et_al_bus_measurements_22371.csv >> /app/public/diff/buskey_et_al_bus_measurements_22371.diff
[CMD] [2020-07-30 15:07:50] echo "." >> /app/public/diff/buskey_et_al_bus_measurements_22371.diff
[STOP] [2020-07-30 15:07:50] calculate_delta
[START] [2020-07-30 15:07:50] parse_diff_and_store
[INFO] [2020-07-30 15:07:50] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 15:07:50] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 15:07:50] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 15:07:50] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 15:07:50] Storing 1 ScientificNames
[INFO] [2020-07-30 15:07:50] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 15:07:50] Average Time: 0.0
[INFO] [2020-07-30 15:07:50] Total Time: 1s
[INFO] [2020-07-30 15:07:50] Storing 1 Nodes
[INFO] [2020-07-30 15:07:50] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 15:07:50] Average Time: 0.0
[INFO] [2020-07-30 15:07:50] Total Time: 1s
[INFO] [2020-07-30 15:07:50] Storing 1 Occurrences
[INFO] [2020-07-30 15:07:50] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 15:07:50] Average Time: 0.0
[INFO] [2020-07-30 15:07:50] Total Time: 1s
[INFO] [2020-07-30 15:07:50] Storing 1 OccurrenceMetadata
[INFO] [2020-07-30 15:07:50] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 15:07:50] Average Time: 0.0
[INFO] [2020-07-30 15:07:50] Total Time: 1s
[INFO] [2020-07-30 15:07:50] Storing 2 Traits
[INFO] [2020-07-30 15:07:50] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 15:07:50] Average Time: 0.0
[INFO] [2020-07-30 15:07:50] Total Time: 1s
[INFO] [2020-07-30 15:07:50] Storing 2 MetaTraits
[INFO] [2020-07-30 15:07:50] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 15:07:50] Average Time: 0.0
[INFO] [2020-07-30 15:07:50] Total Time: 1s
[STOP] [2020-07-30 15:07:50] parse_diff_and_store
[START] [2020-07-30 15:07:50] resolve_keys
[INFO] [2020-07-30 15:07:57] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 15:07:57] traits to occurrences...
[INFO] [2020-07-30 15:07:57] traits to nodes (through occurrences)...
[INFO] [2020-07-30 15:07:57] Traits to sex term...
[INFO] [2020-07-30 15:07:57] Traits to lifestage term...
[INFO] [2020-07-30 15:07:57] MetaTraits to traits...
[INFO] [2020-07-30 15:07:57] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 15:07:57] Assocs to occurrences...
[INFO] [2020-07-30 15:07:57] Assocs to nodes...
[INFO] [2020-07-30 15:07:57] Assoc to sex term...
[INFO] [2020-07-30 15:07:57] Assoc to lifestage term...
[STOP] [2020-07-30 15:07:57] resolve_keys
[START] [2020-07-30 15:07:57] hold_for_later_1
[STOP] [2020-07-30 15:07:57] hold_for_later_1
[START] [2020-07-30 15:07:57] hold_for_later_2
[STOP] [2020-07-30 15:07:57] hold_for_later_2
[START] [2020-07-30 15:07:57] resolve_missing_parents
[STOP] [2020-07-30 15:07:57] resolve_missing_parents
[START] [2020-07-30 15:07:57] rebuild_nodes
[START] [2020-07-30 15:07:57] Flattener#flatten
[START] [2020-07-30 15:07:57] Flattener#study_resource
[START] [2020-07-30 15:07:57] Flattener#build_ancestry
[STOP] [2020-07-30 15:07:57] Flattener#build_ancestry
[INFO] [2020-07-30 15:07:57] 1 ancestry keys
[START] [2020-07-30 15:07:57] build_node_ancestors
[INFO] [2020-07-30 15:07:57] old ancestors deleted.
[STOP] [2020-07-30 15:07:57] build_node_ancestors
[WARN] [2020-07-30 15:07:57] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 15:07:57] Flattener#flatten
[STOP] [2020-07-30 15:07:57] rebuild_nodes
[START] [2020-07-30 15:07:57] resolve_missing_media_owners
[STOP] [2020-07-30 15:07:57] resolve_missing_media_owners
[START] [2020-07-30 15:07:57] sanitize_media_verbatims
[STOP] [2020-07-30 15:07:57] sanitize_media_verbatims
[START] [2020-07-30 15:07:57] queue_downloads
[STOP] [2020-07-30 15:07:57] queue_downloads
[START] [2020-07-30 15:07:57] parse_names
[WARN] [2020-07-30 15:07:57] I see 1 names which still need to be parsed.
[STOP] [2020-07-30 15:07:58] parse_names
[START] [2020-07-30 15:07:58] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 15:07:58] denormalize_canonical_names_to_nodes
[START] [2020-07-30 15:07:58] match_nodes
[START] [2020-07-30 15:07:58] map_all_nodes_to_pages
[STOP] [2020-07-30 15:07:58] map_all_nodes_to_pages
[INFO] [2020-07-30 15:07:58] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-07-30 15:07:58] update_nodes
[STOP] [2020-07-30 15:07:58] update_nodes
[STOP] [2020-07-30 15:07:58] match_nodes
[START] [2020-07-30 15:07:58] reindex_search
[STOP] [2020-07-30 15:07:58] reindex_search
[START] [2020-07-30 15:07:58] normalize_units
[STOP] [2020-07-30 15:07:58] normalize_units
[START] [2020-07-30 15:07:58] calculate_statistics
[2020-07-30 15:07:58] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 15:07:58] calculate_statistics
[START] [2020-07-30 15:07:58] complete_harvest_instance
[START] [2020-07-30 15:07:58] overall_tsv_creation
[INFO] [2020-07-30 15:07:58] Processing group of 1 in 1 batches of 10000
[INFO] [2020-07-30 15:08:46] 1 Traits (unfiltered)...
[INFO] [2020-07-30 15:09:20] 1 Traits (filtered)...
[INFO] [2020-07-30 15:09:20] 0 Associations (filtered)...
[INFO] [2020-07-30 15:09:20] 4 metadata added.
[INFO] [2020-07-30 15:09:20] 0 metadata added.
[INFO] [2020-07-30 15:09:20] Average Time: 55.42
[INFO] [2020-07-30 15:09:20] Total Time: 1m23s
[STOP] [2020-07-30 15:09:20] overall_tsv_creation
[INFO] [2020-07-30 15:09:20] Done. Check your files:
[INFO] [2020-07-30 15:09:20] (1 lines) /app/public/data/buskey_et_al_bus/publish_nodes.tsv
[INFO] [2020-07-30 15:09:20] (1 lines) /app/public/data/buskey_et_al_bus/publish_scientific_names.tsv
[INFO] [2020-07-30 15:09:20] (2 lines) /app/public/data/buskey_et_al_bus/publish_traits.tsv
[INFO] [2020-07-30 15:09:20] (3 lines) /app/public/data/buskey_et_al_bus/publish_metadata.tsv
[STOP] [2020-07-30 15:09:20] complete_harvest_instance
[START] [2020-07-30 15:09:20] completed
[STOP] [2020-07-30 15:09:20] completed
[STOP] [2020-07-30 15:09:20] logged process, took 92.09
Latest Process

30 Jul 15:07 EXITED currently processing 0