Harvest for Smith 1937 Created 30 Jul 12:50

Stage: completed
Fetched: 30 Jul 12:50
Validated: 30 Jul 12:50
Deltas Created 30 Jul 12:50
Units Normalized: 30 Jul 12:50
Ancestry Built: 30 Jul 12:50
Nodes Matched: 30 Jul 12:50
Names Parsed: 30 Jul 12:50
New Models Stored: 30 Jul 12:50
Indexed: 30 Jul 12:50
Completed: 30 Jul 12:51
Time to Harvest: less than a minute
Harvesting Log

(137 lines)
# Logfile created on 2020-07-30 12:49:58 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 12:49:58] logged process
[START] [2020-07-30 12:49:58] Creating resource from OpenData
[START] [2020-07-30 12:49:59] logged process
[START] [2020-07-30 12:49:59] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:49:59] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:49:59] Creating resource from OpenData
[INFO] [2020-07-30 12:50:16] ## HARVEST: type = -harvest
[START] [2020-07-30 12:50:21] logged process
[START] [2020-07-30 12:50:21] create_harvest_instance
[STOP] [2020-07-30 12:50:22] create_harvest_instance
[START] [2020-07-30 12:50:22] fetch_files
[STOP] [2020-07-30 12:50:22] fetch_files
[START] [2020-07-30 12:50:22] validate_each_file
[STOP] [2020-07-30 12:50:23] validate_each_file
[START] [2020-07-30 12:50:23] convert_to_csv
[CMD] [2020-07-30 12:50:23] /usr/bin/sort /app/public/converted_csv/smith_smith_1937_refs_22268.csv > /app/public/converted_csv/smith_smith_1937_refs_22268.csv_sorted
[CMD] [2020-07-30 12:50:23] /usr/bin/sort /app/public/converted_csv/smith_smith_1937_nodes_22269.csv > /app/public/converted_csv/smith_smith_1937_nodes_22269.csv_sorted
[CMD] [2020-07-30 12:50:23] /usr/bin/sort /app/public/converted_csv/smith_smith_1937_occurrences_22270.csv > /app/public/converted_csv/smith_smith_1937_occurrences_22270.csv_sorted
[CMD] [2020-07-30 12:50:23] /usr/bin/sort /app/public/converted_csv/smith_smith_1937_measurements_22271.csv > /app/public/converted_csv/smith_smith_1937_measurements_22271.csv_sorted
[STOP] [2020-07-30 12:50:23] convert_to_csv
[START] [2020-07-30 12:50:23] calculate_delta
[CMD] [2020-07-30 12:50:23] echo "0a" > /app/public/diff/smith_smith_1937_refs_22268.diff
[CMD] [2020-07-30 12:50:23] tail -n +1 /app/public/converted_csv/smith_smith_1937_refs_22268.csv >> /app/public/diff/smith_smith_1937_refs_22268.diff
[CMD] [2020-07-30 12:50:23] echo "." >> /app/public/diff/smith_smith_1937_refs_22268.diff
[CMD] [2020-07-30 12:50:23] echo "0a" > /app/public/diff/smith_smith_1937_nodes_22269.diff
[CMD] [2020-07-30 12:50:23] tail -n +1 /app/public/converted_csv/smith_smith_1937_nodes_22269.csv >> /app/public/diff/smith_smith_1937_nodes_22269.diff
[CMD] [2020-07-30 12:50:23] echo "." >> /app/public/diff/smith_smith_1937_nodes_22269.diff
[CMD] [2020-07-30 12:50:23] echo "0a" > /app/public/diff/smith_smith_1937_occurrences_22270.diff
[CMD] [2020-07-30 12:50:23] tail -n +1 /app/public/converted_csv/smith_smith_1937_occurrences_22270.csv >> /app/public/diff/smith_smith_1937_occurrences_22270.diff
[CMD] [2020-07-30 12:50:23] echo "." >> /app/public/diff/smith_smith_1937_occurrences_22270.diff
[CMD] [2020-07-30 12:50:23] echo "0a" > /app/public/diff/smith_smith_1937_measurements_22271.diff
[CMD] [2020-07-30 12:50:23] tail -n +1 /app/public/converted_csv/smith_smith_1937_measurements_22271.csv >> /app/public/diff/smith_smith_1937_measurements_22271.diff
[CMD] [2020-07-30 12:50:23] echo "." >> /app/public/diff/smith_smith_1937_measurements_22271.diff
[STOP] [2020-07-30 12:50:23] calculate_delta
[START] [2020-07-30 12:50:23] parse_diff_and_store
[INFO] [2020-07-30 12:50:23] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 12:50:23] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 12:50:23] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 12:50:23] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 12:50:23] Storing 4 ScientificNames
[INFO] [2020-07-30 12:50:23] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 12:50:23] Average Time: 0.0
[INFO] [2020-07-30 12:50:23] Total Time: 1s
[INFO] [2020-07-30 12:50:23] Storing 4 Nodes
[INFO] [2020-07-30 12:50:23] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 12:50:23] Average Time: 0.0
[INFO] [2020-07-30 12:50:23] Total Time: 1s
[INFO] [2020-07-30 12:50:23] Storing 4 Occurrences
[INFO] [2020-07-30 12:50:23] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 12:50:23] Average Time: 0.0
[INFO] [2020-07-30 12:50:23] Total Time: 1s
[INFO] [2020-07-30 12:50:23] Storing 12 Traits
[INFO] [2020-07-30 12:50:23] Processing group of 12 in 1 groups of 1000
[INFO] [2020-07-30 12:50:23] Average Time: 0.01
[INFO] [2020-07-30 12:50:23] Total Time: 1s
[INFO] [2020-07-30 12:50:23] Storing 9 MetaTraits
[INFO] [2020-07-30 12:50:23] Processing group of 9 in 1 groups of 1000
[INFO] [2020-07-30 12:50:23] Average Time: 0.0
[INFO] [2020-07-30 12:50:23] Total Time: 1s
[STOP] [2020-07-30 12:50:23] parse_diff_and_store
[START] [2020-07-30 12:50:23] resolve_keys
[INFO] [2020-07-30 12:50:30] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 12:50:30] traits to occurrences...
[INFO] [2020-07-30 12:50:30] traits to nodes (through occurrences)...
[INFO] [2020-07-30 12:50:30] Traits to sex term...
[INFO] [2020-07-30 12:50:30] Traits to lifestage term...
[INFO] [2020-07-30 12:50:30] MetaTraits to traits...
[INFO] [2020-07-30 12:50:30] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 12:50:30] Assocs to occurrences...
[INFO] [2020-07-30 12:50:30] Assocs to nodes...
[INFO] [2020-07-30 12:50:30] Assoc to sex term...
[INFO] [2020-07-30 12:50:30] Assoc to lifestage term...
[STOP] [2020-07-30 12:50:30] resolve_keys
[START] [2020-07-30 12:50:30] hold_for_later_1
[STOP] [2020-07-30 12:50:30] hold_for_later_1
[START] [2020-07-30 12:50:30] hold_for_later_2
[STOP] [2020-07-30 12:50:30] hold_for_later_2
[START] [2020-07-30 12:50:30] resolve_missing_parents
[STOP] [2020-07-30 12:50:30] resolve_missing_parents
[START] [2020-07-30 12:50:30] rebuild_nodes
[START] [2020-07-30 12:50:30] Flattener#flatten
[START] [2020-07-30 12:50:30] Flattener#study_resource
[START] [2020-07-30 12:50:30] Flattener#build_ancestry
[STOP] [2020-07-30 12:50:30] Flattener#build_ancestry
[INFO] [2020-07-30 12:50:30] 4 ancestry keys
[START] [2020-07-30 12:50:30] build_node_ancestors
[INFO] [2020-07-30 12:50:30] old ancestors deleted.
[STOP] [2020-07-30 12:50:30] build_node_ancestors
[WARN] [2020-07-30 12:50:30] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 12:50:30] Flattener#flatten
[STOP] [2020-07-30 12:50:30] rebuild_nodes
[START] [2020-07-30 12:50:30] resolve_missing_media_owners
[STOP] [2020-07-30 12:50:30] resolve_missing_media_owners
[START] [2020-07-30 12:50:30] sanitize_media_verbatims
[STOP] [2020-07-30 12:50:30] sanitize_media_verbatims
[START] [2020-07-30 12:50:30] queue_downloads
[STOP] [2020-07-30 12:50:30] queue_downloads
[START] [2020-07-30 12:50:30] parse_names
[WARN] [2020-07-30 12:50:30] I see 4 names which still need to be parsed.
[STOP] [2020-07-30 12:50:31] parse_names
[START] [2020-07-30 12:50:31] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 12:50:31] denormalize_canonical_names_to_nodes
[START] [2020-07-30 12:50:31] match_nodes
[START] [2020-07-30 12:50:31] map_all_nodes_to_pages
[STOP] [2020-07-30 12:50:31] map_all_nodes_to_pages
[INFO] [2020-07-30 12:50:31] ZERO unmatched nodes (of 4)! Nicely done.
[START] [2020-07-30 12:50:31] update_nodes
[STOP] [2020-07-30 12:50:31] update_nodes
[STOP] [2020-07-30 12:50:31] match_nodes
[START] [2020-07-30 12:50:31] reindex_search
[STOP] [2020-07-30 12:50:31] reindex_search
[START] [2020-07-30 12:50:31] normalize_units
[STOP] [2020-07-30 12:50:31] normalize_units
[START] [2020-07-30 12:50:31] calculate_statistics
[2020-07-30 12:50:31] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 12:50:31] calculate_statistics
[START] [2020-07-30 12:50:31] complete_harvest_instance
[START] [2020-07-30 12:50:31] overall_tsv_creation
[INFO] [2020-07-30 12:50:31] Processing group of 4 in 1 batches of 10000
[INFO] [2020-07-30 12:51:20] 4 Traits (unfiltered)...
[INFO] [2020-07-30 12:51:56] 4 Traits (filtered)...
[INFO] [2020-07-30 12:51:56] 0 Associations (filtered)...
[INFO] [2020-07-30 12:51:56] 17 metadata added.
[INFO] [2020-07-30 12:51:56] 0 metadata added.
[INFO] [2020-07-30 12:51:56] Average Time: 57.62
[INFO] [2020-07-30 12:51:56] Total Time: 1m25s
[STOP] [2020-07-30 12:51:56] overall_tsv_creation
[INFO] [2020-07-30 12:51:56] Done. Check your files:
[INFO] [2020-07-30 12:51:56] (4 lines) /app/public/data/smith_smith_1937/publish_nodes.tsv
[INFO] [2020-07-30 12:51:56] (4 lines) /app/public/data/smith_smith_1937/publish_scientific_names.tsv
[INFO] [2020-07-30 12:51:56] (5 lines) /app/public/data/smith_smith_1937/publish_traits.tsv
[INFO] [2020-07-30 12:51:56] (9 lines) /app/public/data/smith_smith_1937/publish_metadata.tsv
[STOP] [2020-07-30 12:51:56] complete_harvest_instance
[START] [2020-07-30 12:51:56] completed
[STOP] [2020-07-30 12:51:56] completed
[STOP] [2020-07-30 12:51:56] logged process, took 94.76
Latest Process

30 Jul 12:50 EXITED currently processing 0