Harvest for CLARK 2019 Created 30 Jul 14:59

Stage: completed
Fetched: 30 Jul 14:59
Validated: 30 Jul 14:59
Deltas Created 30 Jul 14:59
Units Normalized: 30 Jul 14:59
Ancestry Built: 30 Jul 14:59
Nodes Matched: 30 Jul 14:59
Names Parsed: 30 Jul 14:59
New Models Stored: 30 Jul 14:59
Indexed: 30 Jul 14:59
Completed: 30 Jul 15:00
Time to Harvest: less than a minute
Harvesting Log

(137 lines)
# Logfile created on 2020-07-30 14:58:56 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 14:58:56] logged process
[START] [2020-07-30 14:58:56] Creating resource from OpenData
[START] [2020-07-30 14:58:56] logged process
[START] [2020-07-30 14:58:56] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:58:56] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 14:58:56] Creating resource from OpenData
[INFO] [2020-07-30 14:59:17] ## HARVEST: type = -harvest
[START] [2020-07-30 14:59:18] logged process
[START] [2020-07-30 14:59:18] create_harvest_instance
[STOP] [2020-07-30 14:59:20] create_harvest_instance
[START] [2020-07-30 14:59:20] fetch_files
[STOP] [2020-07-30 14:59:20] fetch_files
[START] [2020-07-30 14:59:20] validate_each_file
[STOP] [2020-07-30 14:59:20] validate_each_file
[START] [2020-07-30 14:59:20] convert_to_csv
[CMD] [2020-07-30 14:59:20] /usr/bin/sort /app/public/converted_csv/clark_2019_clark_refs_22348.csv > /app/public/converted_csv/clark_2019_clark_refs_22348.csv_sorted
[CMD] [2020-07-30 14:59:20] /usr/bin/sort /app/public/converted_csv/clark_2019_clark_nodes_22349.csv > /app/public/converted_csv/clark_2019_clark_nodes_22349.csv_sorted
[CMD] [2020-07-30 14:59:20] /usr/bin/sort /app/public/converted_csv/clark_2019_clark_occurrences_22350.csv > /app/public/converted_csv/clark_2019_clark_occurrences_22350.csv_sorted
[CMD] [2020-07-30 14:59:20] /usr/bin/sort /app/public/converted_csv/clark_2019_clark_measurements_22351.csv > /app/public/converted_csv/clark_2019_clark_measurements_22351.csv_sorted
[STOP] [2020-07-30 14:59:20] convert_to_csv
[START] [2020-07-30 14:59:20] calculate_delta
[CMD] [2020-07-30 14:59:20] echo "0a" > /app/public/diff/clark_2019_clark_refs_22348.diff
[CMD] [2020-07-30 14:59:20] tail -n +1 /app/public/converted_csv/clark_2019_clark_refs_22348.csv >> /app/public/diff/clark_2019_clark_refs_22348.diff
[CMD] [2020-07-30 14:59:20] echo "." >> /app/public/diff/clark_2019_clark_refs_22348.diff
[CMD] [2020-07-30 14:59:20] echo "0a" > /app/public/diff/clark_2019_clark_nodes_22349.diff
[CMD] [2020-07-30 14:59:20] tail -n +1 /app/public/converted_csv/clark_2019_clark_nodes_22349.csv >> /app/public/diff/clark_2019_clark_nodes_22349.diff
[CMD] [2020-07-30 14:59:20] echo "." >> /app/public/diff/clark_2019_clark_nodes_22349.diff
[CMD] [2020-07-30 14:59:20] echo "0a" > /app/public/diff/clark_2019_clark_occurrences_22350.diff
[CMD] [2020-07-30 14:59:20] tail -n +1 /app/public/converted_csv/clark_2019_clark_occurrences_22350.csv >> /app/public/diff/clark_2019_clark_occurrences_22350.diff
[CMD] [2020-07-30 14:59:20] echo "." >> /app/public/diff/clark_2019_clark_occurrences_22350.diff
[CMD] [2020-07-30 14:59:20] echo "0a" > /app/public/diff/clark_2019_clark_measurements_22351.diff
[CMD] [2020-07-30 14:59:20] tail -n +1 /app/public/converted_csv/clark_2019_clark_measurements_22351.csv >> /app/public/diff/clark_2019_clark_measurements_22351.diff
[CMD] [2020-07-30 14:59:20] echo "." >> /app/public/diff/clark_2019_clark_measurements_22351.diff
[STOP] [2020-07-30 14:59:20] calculate_delta
[START] [2020-07-30 14:59:20] parse_diff_and_store
[INFO] [2020-07-30 14:59:20] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 14:59:20] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 14:59:20] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 14:59:20] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 14:59:20] Storing 1 ScientificNames
[INFO] [2020-07-30 14:59:20] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 14:59:20] Average Time: 0.0
[INFO] [2020-07-30 14:59:20] Total Time: 1s
[INFO] [2020-07-30 14:59:20] Storing 1 Nodes
[INFO] [2020-07-30 14:59:20] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 14:59:20] Average Time: 0.0
[INFO] [2020-07-30 14:59:20] Total Time: 1s
[INFO] [2020-07-30 14:59:20] Storing 1 Occurrences
[INFO] [2020-07-30 14:59:20] Processing group of 1 in 1 groups of 1000
[INFO] [2020-07-30 14:59:20] Average Time: 0.0
[INFO] [2020-07-30 14:59:20] Total Time: 1s
[INFO] [2020-07-30 14:59:20] Storing 8 Traits
[INFO] [2020-07-30 14:59:20] Processing group of 8 in 1 groups of 1000
[INFO] [2020-07-30 14:59:20] Average Time: 0.0
[INFO] [2020-07-30 14:59:20] Total Time: 1s
[INFO] [2020-07-30 14:59:20] Storing 4 MetaTraits
[INFO] [2020-07-30 14:59:20] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 14:59:20] Average Time: 0.0
[INFO] [2020-07-30 14:59:20] Total Time: 1s
[STOP] [2020-07-30 14:59:20] parse_diff_and_store
[START] [2020-07-30 14:59:20] resolve_keys
[INFO] [2020-07-30 14:59:27] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 14:59:27] traits to occurrences...
[INFO] [2020-07-30 14:59:27] traits to nodes (through occurrences)...
[INFO] [2020-07-30 14:59:27] Traits to sex term...
[INFO] [2020-07-30 14:59:27] Traits to lifestage term...
[INFO] [2020-07-30 14:59:27] MetaTraits to traits...
[INFO] [2020-07-30 14:59:27] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 14:59:27] Assocs to occurrences...
[INFO] [2020-07-30 14:59:27] Assocs to nodes...
[INFO] [2020-07-30 14:59:27] Assoc to sex term...
[INFO] [2020-07-30 14:59:27] Assoc to lifestage term...
[STOP] [2020-07-30 14:59:27] resolve_keys
[START] [2020-07-30 14:59:27] hold_for_later_1
[STOP] [2020-07-30 14:59:27] hold_for_later_1
[START] [2020-07-30 14:59:27] hold_for_later_2
[STOP] [2020-07-30 14:59:27] hold_for_later_2
[START] [2020-07-30 14:59:27] resolve_missing_parents
[STOP] [2020-07-30 14:59:27] resolve_missing_parents
[START] [2020-07-30 14:59:27] rebuild_nodes
[START] [2020-07-30 14:59:27] Flattener#flatten
[START] [2020-07-30 14:59:27] Flattener#study_resource
[START] [2020-07-30 14:59:27] Flattener#build_ancestry
[STOP] [2020-07-30 14:59:27] Flattener#build_ancestry
[INFO] [2020-07-30 14:59:27] 1 ancestry keys
[START] [2020-07-30 14:59:27] build_node_ancestors
[INFO] [2020-07-30 14:59:27] old ancestors deleted.
[STOP] [2020-07-30 14:59:27] build_node_ancestors
[WARN] [2020-07-30 14:59:27] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 14:59:27] Flattener#flatten
[STOP] [2020-07-30 14:59:27] rebuild_nodes
[START] [2020-07-30 14:59:27] resolve_missing_media_owners
[STOP] [2020-07-30 14:59:27] resolve_missing_media_owners
[START] [2020-07-30 14:59:27] sanitize_media_verbatims
[STOP] [2020-07-30 14:59:27] sanitize_media_verbatims
[START] [2020-07-30 14:59:27] queue_downloads
[STOP] [2020-07-30 14:59:27] queue_downloads
[START] [2020-07-30 14:59:27] parse_names
[WARN] [2020-07-30 14:59:27] I see 1 names which still need to be parsed.
[STOP] [2020-07-30 14:59:28] parse_names
[START] [2020-07-30 14:59:28] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 14:59:28] denormalize_canonical_names_to_nodes
[START] [2020-07-30 14:59:28] match_nodes
[START] [2020-07-30 14:59:28] map_all_nodes_to_pages
[STOP] [2020-07-30 14:59:28] map_all_nodes_to_pages
[INFO] [2020-07-30 14:59:28] ZERO unmatched nodes (of 1)! Nicely done.
[START] [2020-07-30 14:59:28] update_nodes
[STOP] [2020-07-30 14:59:28] update_nodes
[STOP] [2020-07-30 14:59:28] match_nodes
[START] [2020-07-30 14:59:28] reindex_search
[STOP] [2020-07-30 14:59:28] reindex_search
[START] [2020-07-30 14:59:28] normalize_units
[STOP] [2020-07-30 14:59:28] normalize_units
[START] [2020-07-30 14:59:28] calculate_statistics
[2020-07-30 14:59:28] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 14:59:28] calculate_statistics
[START] [2020-07-30 14:59:28] complete_harvest_instance
[START] [2020-07-30 14:59:28] overall_tsv_creation
[INFO] [2020-07-30 14:59:28] Processing group of 1 in 1 batches of 10000
[INFO] [2020-07-30 15:00:16] 2 Traits (unfiltered)...
[INFO] [2020-07-30 15:00:51] 2 Traits (filtered)...
[INFO] [2020-07-30 15:00:51] 0 Associations (filtered)...
[INFO] [2020-07-30 15:00:51] 10 metadata added.
[INFO] [2020-07-30 15:00:51] 0 metadata added.
[INFO] [2020-07-30 15:00:51] Average Time: 55.92
[INFO] [2020-07-30 15:00:51] Total Time: 1m23s
[STOP] [2020-07-30 15:00:51] overall_tsv_creation
[INFO] [2020-07-30 15:00:51] Done. Check your files:
[INFO] [2020-07-30 15:00:51] (1 lines) /app/public/data/clark_2019_clark/publish_nodes.tsv
[INFO] [2020-07-30 15:00:51] (1 lines) /app/public/data/clark_2019_clark/publish_scientific_names.tsv
[INFO] [2020-07-30 15:00:51] (3 lines) /app/public/data/clark_2019_clark/publish_traits.tsv
[INFO] [2020-07-30 15:00:51] (7 lines) /app/public/data/clark_2019_clark/publish_metadata.tsv
[STOP] [2020-07-30 15:00:51] complete_harvest_instance
[START] [2020-07-30 15:00:51] completed
[STOP] [2020-07-30 15:00:51] completed
[STOP] [2020-07-30 15:00:51] logged process, took 92.5
Latest Process

30 Jul 14:59 EXITED currently processing 0