Harvest for Addisonia volume 3 Created 09 Apr 08:32

Stage: completed
Fetched: 09 Apr 08:32
Validated: 09 Apr 08:32
Deltas Created 09 Apr 08:32
Units Normalized: 09 Apr 08:33
Ancestry Built: 09 Apr 08:33
Nodes Matched: 09 Apr 08:33
Names Parsed: 09 Apr 08:33
New Models Stored: 09 Apr 08:32
Indexed: 09 Apr 08:33
Completed: 09 Apr 08:34
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2020-04-09 08:32:53 -0400 by logger.rb/v1.4.2
[INFO] [2020-04-09 08:32:53] ## HARVEST: type = -harvest
[START] [2020-04-09 08:32:57] logged process
[START] [2020-04-09 08:32:57] create_harvest_instance
[STOP] [2020-04-09 08:32:58] create_harvest_instance
[START] [2020-04-09 08:32:58] fetch_files
[STOP] [2020-04-09 08:32:58] fetch_files
[START] [2020-04-09 08:32:58] validate_each_file
[STOP] [2020-04-09 08:32:58] validate_each_file
[START] [2020-04-09 08:32:58] convert_to_csv
[CMD] [2020-04-09 08:32:58] /usr/bin/sort /app/public/converted_csv/addisonia_volum2_agents_20691.csv > /app/public/converted_csv/addisonia_volum2_agents_20691.csv_sorted
[CMD] [2020-04-09 08:32:58] /usr/bin/sort /app/public/converted_csv/addisonia_volum2_nodes_20692.csv > /app/public/converted_csv/addisonia_volum2_nodes_20692.csv_sorted
[CMD] [2020-04-09 08:32:58] /usr/bin/sort /app/public/converted_csv/addisonia_volum2_media_20693.csv > /app/public/converted_csv/addisonia_volum2_media_20693.csv_sorted
[STOP] [2020-04-09 08:32:58] convert_to_csv
[START] [2020-04-09 08:32:58] calculate_delta
[CMD] [2020-04-09 08:32:58] echo "0a" > /app/public/diff/addisonia_volum2_agents_20691.diff
[CMD] [2020-04-09 08:32:59] tail -n +1 /app/public/converted_csv/addisonia_volum2_agents_20691.csv >> /app/public/diff/addisonia_volum2_agents_20691.diff
[CMD] [2020-04-09 08:32:59] echo "." >> /app/public/diff/addisonia_volum2_agents_20691.diff
[CMD] [2020-04-09 08:32:59] echo "0a" > /app/public/diff/addisonia_volum2_nodes_20692.diff
[CMD] [2020-04-09 08:32:59] tail -n +1 /app/public/converted_csv/addisonia_volum2_nodes_20692.csv >> /app/public/diff/addisonia_volum2_nodes_20692.diff
[CMD] [2020-04-09 08:32:59] echo "." >> /app/public/diff/addisonia_volum2_nodes_20692.diff
[CMD] [2020-04-09 08:32:59] echo "0a" > /app/public/diff/addisonia_volum2_media_20693.diff
[CMD] [2020-04-09 08:32:59] tail -n +1 /app/public/converted_csv/addisonia_volum2_media_20693.csv >> /app/public/diff/addisonia_volum2_media_20693.diff
[CMD] [2020-04-09 08:32:59] echo "." >> /app/public/diff/addisonia_volum2_media_20693.diff
[STOP] [2020-04-09 08:32:59] calculate_delta
[START] [2020-04-09 08:32:59] parse_diff_and_store
[INFO] [2020-04-09 08:32:59] Loading agents diff file into memory (true lines)...
[INFO] [2020-04-09 08:32:59] Loading nodes diff file into memory (true lines)...
[INFO] [2020-04-09 08:32:59] Loading media diff file into memory (true lines)...
[INFO] [2020-04-09 08:32:59] Storing 2 Attributions
[INFO] [2020-04-09 08:32:59] Processing group of 2 in 1 groups of 1000
[INFO] [2020-04-09 08:32:59] Average Time: 0.0
[INFO] [2020-04-09 08:32:59] Total Time: 1s
[INFO] [2020-04-09 08:32:59] Storing 40 ScientificNames
[INFO] [2020-04-09 08:32:59] Processing group of 40 in 1 groups of 1000
[INFO] [2020-04-09 08:32:59] Average Time: 0.02
[INFO] [2020-04-09 08:32:59] Total Time: 1s
[INFO] [2020-04-09 08:32:59] Storing 40 Nodes
[INFO] [2020-04-09 08:32:59] Processing group of 40 in 1 groups of 1000
[INFO] [2020-04-09 08:32:59] Average Time: 0.02
[INFO] [2020-04-09 08:32:59] Total Time: 1s
[INFO] [2020-04-09 08:32:59] Storing 80 ContentAttributions
[INFO] [2020-04-09 08:32:59] Processing group of 80 in 1 groups of 1000
[INFO] [2020-04-09 08:32:59] Average Time: 0.03
[INFO] [2020-04-09 08:32:59] Total Time: 1s
[INFO] [2020-04-09 08:32:59] Storing 40 Media
[INFO] [2020-04-09 08:32:59] Processing group of 40 in 1 groups of 1000
[INFO] [2020-04-09 08:32:59] Average Time: 0.02
[INFO] [2020-04-09 08:32:59] Total Time: 1s
[STOP] [2020-04-09 08:32:59] parse_diff_and_store
[START] [2020-04-09 08:32:59] resolve_keys
[INFO] [2020-04-09 08:33:05] Occurrences to nodes (through scientific_names)...
[INFO] [2020-04-09 08:33:05] traits to occurrences...
[INFO] [2020-04-09 08:33:05] traits to nodes (through occurrences)...
[INFO] [2020-04-09 08:33:05] Traits to sex term...
[INFO] [2020-04-09 08:33:05] Traits to lifestage term...
[INFO] [2020-04-09 08:33:05] MetaTraits to traits...
[INFO] [2020-04-09 08:33:05] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-04-09 08:33:05] Assocs to occurrences...
[INFO] [2020-04-09 08:33:05] Assocs to nodes...
[INFO] [2020-04-09 08:33:05] Assoc to sex term...
[INFO] [2020-04-09 08:33:05] Assoc to lifestage term...
[STOP] [2020-04-09 08:33:05] resolve_keys
[START] [2020-04-09 08:33:05] hold_for_later_1
[STOP] [2020-04-09 08:33:05] hold_for_later_1
[START] [2020-04-09 08:33:05] hold_for_later_2
[STOP] [2020-04-09 08:33:05] hold_for_later_2
[START] [2020-04-09 08:33:05] resolve_missing_parents
[STOP] [2020-04-09 08:33:05] resolve_missing_parents
[START] [2020-04-09 08:33:05] rebuild_nodes
[START] [2020-04-09 08:33:05] Flattener#flatten
[START] [2020-04-09 08:33:05] Flattener#study_resource
[START] [2020-04-09 08:33:05] Flattener#build_ancestry
[STOP] [2020-04-09 08:33:05] Flattener#build_ancestry
[INFO] [2020-04-09 08:33:05] 40 ancestry keys
[START] [2020-04-09 08:33:05] build_node_ancestors
[INFO] [2020-04-09 08:33:05] old ancestors deleted.
[STOP] [2020-04-09 08:33:05] build_node_ancestors
[WARN] [2020-04-09 08:33:05] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-04-09 08:33:05] Flattener#flatten
[STOP] [2020-04-09 08:33:05] rebuild_nodes
[START] [2020-04-09 08:33:05] resolve_missing_media_owners
[STOP] [2020-04-09 08:33:05] resolve_missing_media_owners
[START] [2020-04-09 08:33:05] sanitize_media_verbatims
[STOP] [2020-04-09 08:33:05] sanitize_media_verbatims
[START] [2020-04-09 08:33:05] queue_downloads
[STOP] [2020-04-09 08:33:05] queue_downloads
[START] [2020-04-09 08:33:05] parse_names
[WARN] [2020-04-09 08:33:05] I see 40 names which still need to be parsed.
[STOP] [2020-04-09 08:33:07] parse_names
[START] [2020-04-09 08:33:07] denormalize_canonical_names_to_nodes
[STOP] [2020-04-09 08:33:07] denormalize_canonical_names_to_nodes
[START] [2020-04-09 08:33:07] match_nodes
[START] [2020-04-09 08:33:07] map_all_nodes_to_pages
[STOP] [2020-04-09 08:33:10] map_all_nodes_to_pages
[INFO] [2020-04-09 08:33:10] Unmatched nodes (6 of 40): Othonna crassifolia (#68219704); Hammelis (#68219709); Symphyotrichum laeve laeve (#68219712); euphorbia (#68219714); Spiraea thunbergii (#68219723); Aronia prunifolia (#68219737)
[START] [2020-04-09 08:33:10] update_nodes
[STOP] [2020-04-09 08:33:10] update_nodes
[STOP] [2020-04-09 08:33:10] match_nodes
[START] [2020-04-09 08:33:10] reindex_search
[STOP] [2020-04-09 08:33:10] reindex_search
[START] [2020-04-09 08:33:10] normalize_units
[STOP] [2020-04-09 08:33:10] normalize_units
[START] [2020-04-09 08:33:10] calculate_statistics
[2020-04-09 08:33:10] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-04-09 08:33:10] calculate_statistics
[START] [2020-04-09 08:33:10] complete_harvest_instance
[START] [2020-04-09 08:33:10] overall_tsv_creation
[INFO] [2020-04-09 08:33:10] Processing group of 40 in 1 batches of 10000
[INFO] [2020-04-09 08:34:31] Average Time: 21.49
[INFO] [2020-04-09 08:34:31] Total Time: 1m21s
[STOP] [2020-04-09 08:34:31] overall_tsv_creation
[INFO] [2020-04-09 08:34:31] Done. Check your files:
[INFO] [2020-04-09 08:34:31] (40 lines) /app/public/data/addisonia_volum2/publish_nodes.tsv
[INFO] [2020-04-09 08:34:31] (40 lines) /app/public/data/addisonia_volum2/publish_scientific_names.tsv
[INFO] [2020-04-09 08:34:31] (40 lines) /app/public/data/addisonia_volum2/publish_media.tsv
[INFO] [2020-04-09 08:34:31] (15 lines) /app/public/data/addisonia_volum2/publish_image_info.tsv
[INFO] [2020-04-09 08:34:31] (80 lines) /app/public/data/addisonia_volum2/publish_attributions.tsv
[STOP] [2020-04-09 08:34:31] complete_harvest_instance
[START] [2020-04-09 08:34:31] completed
[STOP] [2020-04-09 08:34:31] completed
[STOP] [2020-04-09 08:34:31] logged process, took 93.78

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