Harvest for Kolasa and Tyler 2010 Created 30 Jul 12:29

Stage: completed
Fetched: 30 Jul 12:29
Validated: 30 Jul 12:29
Deltas Created 30 Jul 12:29
Units Normalized: 30 Jul 12:29
Ancestry Built: 30 Jul 12:29
Nodes Matched: 30 Jul 12:29
Names Parsed: 30 Jul 12:29
New Models Stored: 30 Jul 12:29
Indexed: 30 Jul 12:29
Completed: 30 Jul 12:30
Time to Harvest: less than a minute

Harvesting Log (most recent first)

# Logfile created on 2020-07-30 12:25:18 -0400 by logger.rb/v1.4.2
[START] [2020-07-30 12:25:18] logged process
[START] [2020-07-30 12:25:18] Creating resource from OpenData
[START] [2020-07-30 12:25:18] logged process
[START] [2020-07-30 12:25:18] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:25:19] Parse meta.xml file and create formats with fields
[STOP] [2020-07-30 12:25:19] Creating resource from OpenData
[INFO] [2020-07-30 12:29:01] ## HARVEST: type = -harvest
[START] [2020-07-30 12:29:06] logged process
[START] [2020-07-30 12:29:06] create_harvest_instance
[STOP] [2020-07-30 12:29:07] create_harvest_instance
[START] [2020-07-30 12:29:07] fetch_files
[STOP] [2020-07-30 12:29:07] fetch_files
[START] [2020-07-30 12:29:07] validate_each_file
[STOP] [2020-07-30 12:29:07] validate_each_file
[START] [2020-07-30 12:29:07] convert_to_csv
[CMD] [2020-07-30 12:29:07] /usr/bin/sort /app/public/converted_csv/kolasa_tyler_kol_refs_22208.csv > /app/public/converted_csv/kolasa_tyler_kol_refs_22208.csv_sorted
[CMD] [2020-07-30 12:29:07] /usr/bin/sort /app/public/converted_csv/kolasa_tyler_kol_nodes_22209.csv > /app/public/converted_csv/kolasa_tyler_kol_nodes_22209.csv_sorted
[CMD] [2020-07-30 12:29:07] /usr/bin/sort /app/public/converted_csv/kolasa_tyler_kol_occurrences_22210.csv > /app/public/converted_csv/kolasa_tyler_kol_occurrences_22210.csv_sorted
[CMD] [2020-07-30 12:29:07] /usr/bin/sort /app/public/converted_csv/kolasa_tyler_kol_measurements_22211.csv > /app/public/converted_csv/kolasa_tyler_kol_measurements_22211.csv_sorted
[STOP] [2020-07-30 12:29:07] convert_to_csv
[START] [2020-07-30 12:29:07] calculate_delta
[CMD] [2020-07-30 12:29:07] echo "0a" > /app/public/diff/kolasa_tyler_kol_refs_22208.diff
[CMD] [2020-07-30 12:29:07] tail -n +1 /app/public/converted_csv/kolasa_tyler_kol_refs_22208.csv >> /app/public/diff/kolasa_tyler_kol_refs_22208.diff
[CMD] [2020-07-30 12:29:07] echo "." >> /app/public/diff/kolasa_tyler_kol_refs_22208.diff
[CMD] [2020-07-30 12:29:07] echo "0a" > /app/public/diff/kolasa_tyler_kol_nodes_22209.diff
[CMD] [2020-07-30 12:29:07] tail -n +1 /app/public/converted_csv/kolasa_tyler_kol_nodes_22209.csv >> /app/public/diff/kolasa_tyler_kol_nodes_22209.diff
[CMD] [2020-07-30 12:29:07] echo "." >> /app/public/diff/kolasa_tyler_kol_nodes_22209.diff
[CMD] [2020-07-30 12:29:07] echo "0a" > /app/public/diff/kolasa_tyler_kol_occurrences_22210.diff
[CMD] [2020-07-30 12:29:07] tail -n +1 /app/public/converted_csv/kolasa_tyler_kol_occurrences_22210.csv >> /app/public/diff/kolasa_tyler_kol_occurrences_22210.diff
[CMD] [2020-07-30 12:29:07] echo "." >> /app/public/diff/kolasa_tyler_kol_occurrences_22210.diff
[CMD] [2020-07-30 12:29:07] echo "0a" > /app/public/diff/kolasa_tyler_kol_measurements_22211.diff
[CMD] [2020-07-30 12:29:07] tail -n +1 /app/public/converted_csv/kolasa_tyler_kol_measurements_22211.csv >> /app/public/diff/kolasa_tyler_kol_measurements_22211.diff
[CMD] [2020-07-30 12:29:07] echo "." >> /app/public/diff/kolasa_tyler_kol_measurements_22211.diff
[STOP] [2020-07-30 12:29:07] calculate_delta
[START] [2020-07-30 12:29:07] parse_diff_and_store
[INFO] [2020-07-30 12:29:07] Loading refs diff file into memory (true lines)...
[INFO] [2020-07-30 12:29:07] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-30 12:29:07] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-30 12:29:07] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-30 12:29:07] Storing 2 ScientificNames
[INFO] [2020-07-30 12:29:07] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 12:29:07] Average Time: 0.0
[INFO] [2020-07-30 12:29:07] Total Time: 1s
[INFO] [2020-07-30 12:29:07] Storing 2 Nodes
[INFO] [2020-07-30 12:29:07] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 12:29:07] Average Time: 0.0
[INFO] [2020-07-30 12:29:07] Total Time: 1s
[INFO] [2020-07-30 12:29:07] Storing 2 Occurrences
[INFO] [2020-07-30 12:29:07] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-30 12:29:07] Average Time: 0.0
[INFO] [2020-07-30 12:29:07] Total Time: 1s
[INFO] [2020-07-30 12:29:07] Storing 4 Traits
[INFO] [2020-07-30 12:29:07] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 12:29:07] Average Time: 0.0
[INFO] [2020-07-30 12:29:07] Total Time: 1s
[INFO] [2020-07-30 12:29:07] Storing 4 MetaTraits
[INFO] [2020-07-30 12:29:07] Processing group of 4 in 1 groups of 1000
[INFO] [2020-07-30 12:29:07] Average Time: 0.0
[INFO] [2020-07-30 12:29:07] Total Time: 1s
[STOP] [2020-07-30 12:29:07] parse_diff_and_store
[START] [2020-07-30 12:29:07] resolve_keys
[INFO] [2020-07-30 12:29:14] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-30 12:29:14] traits to occurrences...
[INFO] [2020-07-30 12:29:14] traits to nodes (through occurrences)...
[INFO] [2020-07-30 12:29:14] Traits to sex term...
[INFO] [2020-07-30 12:29:14] Traits to lifestage term...
[INFO] [2020-07-30 12:29:14] MetaTraits to traits...
[INFO] [2020-07-30 12:29:14] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-30 12:29:14] Assocs to occurrences...
[INFO] [2020-07-30 12:29:14] Assocs to nodes...
[INFO] [2020-07-30 12:29:14] Assoc to sex term...
[INFO] [2020-07-30 12:29:14] Assoc to lifestage term...
[STOP] [2020-07-30 12:29:14] resolve_keys
[START] [2020-07-30 12:29:14] hold_for_later_1
[STOP] [2020-07-30 12:29:14] hold_for_later_1
[START] [2020-07-30 12:29:14] hold_for_later_2
[STOP] [2020-07-30 12:29:14] hold_for_later_2
[START] [2020-07-30 12:29:14] resolve_missing_parents
[STOP] [2020-07-30 12:29:14] resolve_missing_parents
[START] [2020-07-30 12:29:14] rebuild_nodes
[START] [2020-07-30 12:29:14] Flattener#flatten
[START] [2020-07-30 12:29:14] Flattener#study_resource
[START] [2020-07-30 12:29:14] Flattener#build_ancestry
[STOP] [2020-07-30 12:29:14] Flattener#build_ancestry
[INFO] [2020-07-30 12:29:14] 2 ancestry keys
[START] [2020-07-30 12:29:14] build_node_ancestors
[INFO] [2020-07-30 12:29:14] old ancestors deleted.
[STOP] [2020-07-30 12:29:14] build_node_ancestors
[WARN] [2020-07-30 12:29:14] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-30 12:29:14] Flattener#flatten
[STOP] [2020-07-30 12:29:14] rebuild_nodes
[START] [2020-07-30 12:29:14] resolve_missing_media_owners
[STOP] [2020-07-30 12:29:14] resolve_missing_media_owners
[START] [2020-07-30 12:29:14] sanitize_media_verbatims
[STOP] [2020-07-30 12:29:14] sanitize_media_verbatims
[START] [2020-07-30 12:29:14] queue_downloads
[STOP] [2020-07-30 12:29:14] queue_downloads
[START] [2020-07-30 12:29:14] parse_names
[WARN] [2020-07-30 12:29:14] I see 2 names which still need to be parsed.
[STOP] [2020-07-30 12:29:15] parse_names
[START] [2020-07-30 12:29:15] denormalize_canonical_names_to_nodes
[STOP] [2020-07-30 12:29:15] denormalize_canonical_names_to_nodes
[START] [2020-07-30 12:29:15] match_nodes
[START] [2020-07-30 12:29:15] map_all_nodes_to_pages
[STOP] [2020-07-30 12:29:15] map_all_nodes_to_pages
[INFO] [2020-07-30 12:29:15] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2020-07-30 12:29:15] update_nodes
[STOP] [2020-07-30 12:29:16] update_nodes
[STOP] [2020-07-30 12:29:16] match_nodes
[START] [2020-07-30 12:29:16] reindex_search
[STOP] [2020-07-30 12:29:16] reindex_search
[START] [2020-07-30 12:29:16] normalize_units
[STOP] [2020-07-30 12:29:16] normalize_units
[START] [2020-07-30 12:29:16] calculate_statistics
[2020-07-30 12:29:16] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-30 12:29:16] calculate_statistics
[START] [2020-07-30 12:29:16] complete_harvest_instance
[START] [2020-07-30 12:29:16] overall_tsv_creation
[INFO] [2020-07-30 12:29:16] Processing group of 2 in 1 batches of 10000
[INFO] [2020-07-30 12:30:05] 2 Traits (unfiltered)...
[INFO] [2020-07-30 12:30:43] 2 Traits (filtered)...
[INFO] [2020-07-30 12:30:43] 0 Associations (filtered)...
[INFO] [2020-07-30 12:30:43] 6 metadata added.
[INFO] [2020-07-30 12:30:43] 0 metadata added.
[INFO] [2020-07-30 12:30:43] Average Time: 59.37
[INFO] [2020-07-30 12:30:43] Total Time: 1m27s
[STOP] [2020-07-30 12:30:43] overall_tsv_creation
[INFO] [2020-07-30 12:30:43] Done. Check your files:
[INFO] [2020-07-30 12:30:43] (2 lines) /app/public/data/kolasa_tyler_kol/publish_nodes.tsv
[INFO] [2020-07-30 12:30:43] (2 lines) /app/public/data/kolasa_tyler_kol/publish_scientific_names.tsv
[INFO] [2020-07-30 12:30:43] (3 lines) /app/public/data/kolasa_tyler_kol/publish_traits.tsv
[INFO] [2020-07-30 12:30:43] (3 lines) /app/public/data/kolasa_tyler_kol/publish_metadata.tsv
[STOP] [2020-07-30 12:30:43] complete_harvest_instance
[START] [2020-07-30 12:30:43] completed
[STOP] [2020-07-30 12:30:43] completed
[STOP] [2020-07-30 12:30:43] logged process, took 97.0

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