Harvest for Johnsgard 1962 Created 22 Jul 15:21

Stage: completed
Fetched: 22 Jul 15:21
Validated: 22 Jul 15:21
Deltas Created 22 Jul 15:21
Units Normalized: 22 Jul 15:22
Ancestry Built: 22 Jul 15:22
Nodes Matched: 22 Jul 15:22
Names Parsed: 22 Jul 15:22
New Models Stored: 22 Jul 15:21
Indexed: 22 Jul 15:22
Completed: 22 Jul 15:23
Time to Harvest: less than a minute
Harvesting Log

(132 lines)
# Logfile created on 2020-07-22 15:18:21 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 15:18:21] logged process
[START] [2020-07-22 15:18:21] Creating resource from OpenData
[START] [2020-07-22 15:18:22] logged process
[START] [2020-07-22 15:18:22] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:18:22] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:18:22] Creating resource from OpenData
[INFO] [2020-07-22 15:21:52] ## HARVEST: type = -harvest
[START] [2020-07-22 15:21:54] logged process
[START] [2020-07-22 15:21:54] create_harvest_instance
[STOP] [2020-07-22 15:21:55] create_harvest_instance
[START] [2020-07-22 15:21:55] fetch_files
[STOP] [2020-07-22 15:21:55] fetch_files
[START] [2020-07-22 15:21:55] validate_each_file
[STOP] [2020-07-22 15:21:55] validate_each_file
[START] [2020-07-22 15:21:55] convert_to_csv
[CMD] [2020-07-22 15:21:55] /usr/bin/sort /app/public/converted_csv/johnsgard_johnsg_nodes_22078.csv > /app/public/converted_csv/johnsgard_johnsg_nodes_22078.csv_sorted
[CMD] [2020-07-22 15:21:55] /usr/bin/sort /app/public/converted_csv/johnsgard_johnsg_occurrences_22079.csv > /app/public/converted_csv/johnsgard_johnsg_occurrences_22079.csv_sorted
[CMD] [2020-07-22 15:21:55] /usr/bin/sort /app/public/converted_csv/johnsgard_johnsg_measurements_22080.csv > /app/public/converted_csv/johnsgard_johnsg_measurements_22080.csv_sorted
[STOP] [2020-07-22 15:21:55] convert_to_csv
[START] [2020-07-22 15:21:55] calculate_delta
[CMD] [2020-07-22 15:21:55] echo "0a" > /app/public/diff/johnsgard_johnsg_nodes_22078.diff
[CMD] [2020-07-22 15:21:55] tail -n +1 /app/public/converted_csv/johnsgard_johnsg_nodes_22078.csv >> /app/public/diff/johnsgard_johnsg_nodes_22078.diff
[CMD] [2020-07-22 15:21:55] echo "." >> /app/public/diff/johnsgard_johnsg_nodes_22078.diff
[CMD] [2020-07-22 15:21:55] echo "0a" > /app/public/diff/johnsgard_johnsg_occurrences_22079.diff
[CMD] [2020-07-22 15:21:55] tail -n +1 /app/public/converted_csv/johnsgard_johnsg_occurrences_22079.csv >> /app/public/diff/johnsgard_johnsg_occurrences_22079.diff
[CMD] [2020-07-22 15:21:55] echo "." >> /app/public/diff/johnsgard_johnsg_occurrences_22079.diff
[CMD] [2020-07-22 15:21:55] echo "0a" > /app/public/diff/johnsgard_johnsg_measurements_22080.diff
[CMD] [2020-07-22 15:21:55] tail -n +1 /app/public/converted_csv/johnsgard_johnsg_measurements_22080.csv >> /app/public/diff/johnsgard_johnsg_measurements_22080.diff
[CMD] [2020-07-22 15:21:55] echo "." >> /app/public/diff/johnsgard_johnsg_measurements_22080.diff
[STOP] [2020-07-22 15:21:55] calculate_delta
[START] [2020-07-22 15:21:55] parse_diff_and_store
[INFO] [2020-07-22 15:21:55] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 15:21:55] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 15:21:55] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 15:21:55] Storing 2 ScientificNames
[INFO] [2020-07-22 15:21:55] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 15:21:55] Average Time: 0.0
[INFO] [2020-07-22 15:21:55] Total Time: 1s
[INFO] [2020-07-22 15:21:55] Storing 2 Nodes
[INFO] [2020-07-22 15:21:55] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 15:21:55] Average Time: 0.0
[INFO] [2020-07-22 15:21:55] Total Time: 1s
[INFO] [2020-07-22 15:21:55] Storing 2 Occurrences
[INFO] [2020-07-22 15:21:55] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 15:21:56] Average Time: 0.0
[INFO] [2020-07-22 15:21:56] Total Time: 1s
[INFO] [2020-07-22 15:21:56] Storing 5 Traits
[INFO] [2020-07-22 15:21:56] Processing group of 5 in 1 groups of 1000
[INFO] [2020-07-22 15:21:56] Average Time: 0.0
[INFO] [2020-07-22 15:21:56] Total Time: 1s
[INFO] [2020-07-22 15:21:56] Storing 6 MetaTraits
[INFO] [2020-07-22 15:21:56] Processing group of 6 in 1 groups of 1000
[INFO] [2020-07-22 15:21:56] Average Time: 0.0
[INFO] [2020-07-22 15:21:56] Total Time: 1s
[STOP] [2020-07-22 15:21:56] parse_diff_and_store
[START] [2020-07-22 15:21:56] resolve_keys
[INFO] [2020-07-22 15:22:02] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 15:22:02] traits to occurrences...
[INFO] [2020-07-22 15:22:02] traits to nodes (through occurrences)...
[INFO] [2020-07-22 15:22:02] Traits to sex term...
[INFO] [2020-07-22 15:22:02] Traits to lifestage term...
[INFO] [2020-07-22 15:22:02] MetaTraits to traits...
[INFO] [2020-07-22 15:22:02] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 15:22:02] Assocs to occurrences...
[INFO] [2020-07-22 15:22:02] Assocs to nodes...
[INFO] [2020-07-22 15:22:02] Assoc to sex term...
[INFO] [2020-07-22 15:22:02] Assoc to lifestage term...
[STOP] [2020-07-22 15:22:02] resolve_keys
[START] [2020-07-22 15:22:02] hold_for_later_1
[STOP] [2020-07-22 15:22:02] hold_for_later_1
[START] [2020-07-22 15:22:02] hold_for_later_2
[STOP] [2020-07-22 15:22:02] hold_for_later_2
[START] [2020-07-22 15:22:02] resolve_missing_parents
[STOP] [2020-07-22 15:22:02] resolve_missing_parents
[START] [2020-07-22 15:22:02] rebuild_nodes
[START] [2020-07-22 15:22:02] Flattener#flatten
[START] [2020-07-22 15:22:02] Flattener#study_resource
[START] [2020-07-22 15:22:02] Flattener#build_ancestry
[STOP] [2020-07-22 15:22:02] Flattener#build_ancestry
[INFO] [2020-07-22 15:22:02] 2 ancestry keys
[START] [2020-07-22 15:22:02] build_node_ancestors
[INFO] [2020-07-22 15:22:02] old ancestors deleted.
[STOP] [2020-07-22 15:22:02] build_node_ancestors
[WARN] [2020-07-22 15:22:02] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 15:22:02] Flattener#flatten
[STOP] [2020-07-22 15:22:02] rebuild_nodes
[START] [2020-07-22 15:22:02] resolve_missing_media_owners
[STOP] [2020-07-22 15:22:02] resolve_missing_media_owners
[START] [2020-07-22 15:22:02] sanitize_media_verbatims
[STOP] [2020-07-22 15:22:02] sanitize_media_verbatims
[START] [2020-07-22 15:22:02] queue_downloads
[STOP] [2020-07-22 15:22:02] queue_downloads
[START] [2020-07-22 15:22:02] parse_names
[WARN] [2020-07-22 15:22:02] I see 2 names which still need to be parsed.
[STOP] [2020-07-22 15:22:03] parse_names
[START] [2020-07-22 15:22:03] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 15:22:03] denormalize_canonical_names_to_nodes
[START] [2020-07-22 15:22:03] match_nodes
[START] [2020-07-22 15:22:03] map_all_nodes_to_pages
[STOP] [2020-07-22 15:22:03] map_all_nodes_to_pages
[INFO] [2020-07-22 15:22:03] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2020-07-22 15:22:03] update_nodes
[STOP] [2020-07-22 15:22:03] update_nodes
[STOP] [2020-07-22 15:22:03] match_nodes
[START] [2020-07-22 15:22:03] reindex_search
[STOP] [2020-07-22 15:22:03] reindex_search
[START] [2020-07-22 15:22:03] normalize_units
[STOP] [2020-07-22 15:22:03] normalize_units
[START] [2020-07-22 15:22:03] calculate_statistics
[2020-07-22 15:22:03] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 15:22:03] calculate_statistics
[START] [2020-07-22 15:22:03] complete_harvest_instance
[START] [2020-07-22 15:22:03] overall_tsv_creation
[INFO] [2020-07-22 15:22:03] Processing group of 2 in 1 batches of 10000
[INFO] [2020-07-22 15:22:52] 2 Traits (unfiltered)...
[INFO] [2020-07-22 15:23:27] 2 Traits (filtered)...
[INFO] [2020-07-22 15:23:27] 0 Associations (filtered)...
[INFO] [2020-07-22 15:23:27] 9 metadata added.
[INFO] [2020-07-22 15:23:27] 0 metadata added.
[INFO] [2020-07-22 15:23:27] Average Time: 57.23
[INFO] [2020-07-22 15:23:27] Total Time: 1m25s
[STOP] [2020-07-22 15:23:27] overall_tsv_creation
[INFO] [2020-07-22 15:23:27] Done. Check your files:
[INFO] [2020-07-22 15:23:27] (2 lines) /app/public/data/johnsgard_johnsg/publish_nodes.tsv
[INFO] [2020-07-22 15:23:27] (2 lines) /app/public/data/johnsgard_johnsg/publish_scientific_names.tsv
[INFO] [2020-07-22 15:23:27] (3 lines) /app/public/data/johnsgard_johnsg/publish_traits.tsv
[INFO] [2020-07-22 15:23:27] (4 lines) /app/public/data/johnsgard_johnsg/publish_metadata.tsv
[STOP] [2020-07-22 15:23:28] complete_harvest_instance
[START] [2020-07-22 15:23:28] completed
[STOP] [2020-07-22 15:23:28] completed
[STOP] [2020-07-22 15:23:28] logged process, took 93.43
Latest Process

22 Jul 15:21 EXITED currently processing 0