Harvest for Snyder 1952 Created 22 Jul 15:10

Stage: completed
Fetched: 22 Jul 15:10
Validated: 22 Jul 15:10
Deltas Created 22 Jul 15:10
Units Normalized: 22 Jul 15:10
Ancestry Built: 22 Jul 15:10
Nodes Matched: 22 Jul 15:10
Names Parsed: 22 Jul 15:10
New Models Stored: 22 Jul 15:10
Indexed: 22 Jul 15:10
Completed: 22 Jul 15:12
Time to Harvest: less than a minute
Harvesting Log

(132 lines)
# Logfile created on 2020-07-22 15:07:45 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 15:07:45] logged process
[START] [2020-07-22 15:07:45] Creating resource from OpenData
[START] [2020-07-22 15:07:45] logged process
[START] [2020-07-22 15:07:45] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:07:45] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:07:45] Creating resource from OpenData
[INFO] [2020-07-22 15:10:26] ## HARVEST: type = -harvest
[START] [2020-07-22 15:10:27] logged process
[START] [2020-07-22 15:10:27] create_harvest_instance
[STOP] [2020-07-22 15:10:28] create_harvest_instance
[START] [2020-07-22 15:10:28] fetch_files
[STOP] [2020-07-22 15:10:28] fetch_files
[START] [2020-07-22 15:10:28] validate_each_file
[STOP] [2020-07-22 15:10:29] validate_each_file
[START] [2020-07-22 15:10:29] convert_to_csv
[CMD] [2020-07-22 15:10:29] /usr/bin/sort /app/public/converted_csv/snyder_snyder_19_nodes_22048.csv > /app/public/converted_csv/snyder_snyder_19_nodes_22048.csv_sorted
[CMD] [2020-07-22 15:10:29] /usr/bin/sort /app/public/converted_csv/snyder_snyder_19_occurrences_22049.csv > /app/public/converted_csv/snyder_snyder_19_occurrences_22049.csv_sorted
[CMD] [2020-07-22 15:10:29] /usr/bin/sort /app/public/converted_csv/snyder_snyder_19_measurements_22050.csv > /app/public/converted_csv/snyder_snyder_19_measurements_22050.csv_sorted
[STOP] [2020-07-22 15:10:29] convert_to_csv
[START] [2020-07-22 15:10:29] calculate_delta
[CMD] [2020-07-22 15:10:29] echo "0a" > /app/public/diff/snyder_snyder_19_nodes_22048.diff
[CMD] [2020-07-22 15:10:29] tail -n +1 /app/public/converted_csv/snyder_snyder_19_nodes_22048.csv >> /app/public/diff/snyder_snyder_19_nodes_22048.diff
[CMD] [2020-07-22 15:10:29] echo "." >> /app/public/diff/snyder_snyder_19_nodes_22048.diff
[CMD] [2020-07-22 15:10:29] echo "0a" > /app/public/diff/snyder_snyder_19_occurrences_22049.diff
[CMD] [2020-07-22 15:10:29] tail -n +1 /app/public/converted_csv/snyder_snyder_19_occurrences_22049.csv >> /app/public/diff/snyder_snyder_19_occurrences_22049.diff
[CMD] [2020-07-22 15:10:29] echo "." >> /app/public/diff/snyder_snyder_19_occurrences_22049.diff
[CMD] [2020-07-22 15:10:29] echo "0a" > /app/public/diff/snyder_snyder_19_measurements_22050.diff
[CMD] [2020-07-22 15:10:29] tail -n +1 /app/public/converted_csv/snyder_snyder_19_measurements_22050.csv >> /app/public/diff/snyder_snyder_19_measurements_22050.diff
[CMD] [2020-07-22 15:10:29] echo "." >> /app/public/diff/snyder_snyder_19_measurements_22050.diff
[STOP] [2020-07-22 15:10:29] calculate_delta
[START] [2020-07-22 15:10:29] parse_diff_and_store
[INFO] [2020-07-22 15:10:29] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 15:10:29] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 15:10:29] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 15:10:29] Storing 12 ScientificNames
[INFO] [2020-07-22 15:10:29] Processing group of 12 in 1 groups of 1000
[INFO] [2020-07-22 15:10:29] Average Time: 0.01
[INFO] [2020-07-22 15:10:29] Total Time: 1s
[INFO] [2020-07-22 15:10:29] Storing 12 Nodes
[INFO] [2020-07-22 15:10:29] Processing group of 12 in 1 groups of 1000
[INFO] [2020-07-22 15:10:29] Average Time: 0.0
[INFO] [2020-07-22 15:10:29] Total Time: 1s
[INFO] [2020-07-22 15:10:29] Storing 12 Occurrences
[INFO] [2020-07-22 15:10:29] Processing group of 12 in 1 groups of 1000
[INFO] [2020-07-22 15:10:29] Average Time: 0.0
[INFO] [2020-07-22 15:10:29] Total Time: 1s
[INFO] [2020-07-22 15:10:29] Storing 15 Traits
[INFO] [2020-07-22 15:10:29] Processing group of 15 in 1 groups of 1000
[INFO] [2020-07-22 15:10:29] Average Time: 0.01
[INFO] [2020-07-22 15:10:29] Total Time: 1s
[INFO] [2020-07-22 15:10:29] Storing 24 MetaTraits
[INFO] [2020-07-22 15:10:29] Processing group of 24 in 1 groups of 1000
[INFO] [2020-07-22 15:10:29] Average Time: 0.0
[INFO] [2020-07-22 15:10:29] Total Time: 1s
[STOP] [2020-07-22 15:10:29] parse_diff_and_store
[START] [2020-07-22 15:10:29] resolve_keys
[INFO] [2020-07-22 15:10:36] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 15:10:36] traits to occurrences...
[INFO] [2020-07-22 15:10:36] traits to nodes (through occurrences)...
[INFO] [2020-07-22 15:10:36] Traits to sex term...
[INFO] [2020-07-22 15:10:36] Traits to lifestage term...
[INFO] [2020-07-22 15:10:36] MetaTraits to traits...
[INFO] [2020-07-22 15:10:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 15:10:36] Assocs to occurrences...
[INFO] [2020-07-22 15:10:36] Assocs to nodes...
[INFO] [2020-07-22 15:10:36] Assoc to sex term...
[INFO] [2020-07-22 15:10:36] Assoc to lifestage term...
[STOP] [2020-07-22 15:10:36] resolve_keys
[START] [2020-07-22 15:10:36] hold_for_later_1
[STOP] [2020-07-22 15:10:36] hold_for_later_1
[START] [2020-07-22 15:10:36] hold_for_later_2
[STOP] [2020-07-22 15:10:36] hold_for_later_2
[START] [2020-07-22 15:10:36] resolve_missing_parents
[STOP] [2020-07-22 15:10:36] resolve_missing_parents
[START] [2020-07-22 15:10:36] rebuild_nodes
[START] [2020-07-22 15:10:36] Flattener#flatten
[START] [2020-07-22 15:10:36] Flattener#study_resource
[START] [2020-07-22 15:10:36] Flattener#build_ancestry
[STOP] [2020-07-22 15:10:36] Flattener#build_ancestry
[INFO] [2020-07-22 15:10:36] 12 ancestry keys
[START] [2020-07-22 15:10:36] build_node_ancestors
[INFO] [2020-07-22 15:10:36] old ancestors deleted.
[STOP] [2020-07-22 15:10:36] build_node_ancestors
[WARN] [2020-07-22 15:10:36] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 15:10:36] Flattener#flatten
[STOP] [2020-07-22 15:10:36] rebuild_nodes
[START] [2020-07-22 15:10:36] resolve_missing_media_owners
[STOP] [2020-07-22 15:10:36] resolve_missing_media_owners
[START] [2020-07-22 15:10:36] sanitize_media_verbatims
[STOP] [2020-07-22 15:10:36] sanitize_media_verbatims
[START] [2020-07-22 15:10:36] queue_downloads
[STOP] [2020-07-22 15:10:36] queue_downloads
[START] [2020-07-22 15:10:36] parse_names
[WARN] [2020-07-22 15:10:36] I see 12 names which still need to be parsed.
[STOP] [2020-07-22 15:10:37] parse_names
[START] [2020-07-22 15:10:37] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 15:10:37] denormalize_canonical_names_to_nodes
[START] [2020-07-22 15:10:37] match_nodes
[START] [2020-07-22 15:10:37] map_all_nodes_to_pages
[STOP] [2020-07-22 15:10:37] map_all_nodes_to_pages
[INFO] [2020-07-22 15:10:37] ZERO unmatched nodes (of 12)! Nicely done.
[START] [2020-07-22 15:10:37] update_nodes
[STOP] [2020-07-22 15:10:37] update_nodes
[STOP] [2020-07-22 15:10:37] match_nodes
[START] [2020-07-22 15:10:37] reindex_search
[STOP] [2020-07-22 15:10:37] reindex_search
[START] [2020-07-22 15:10:37] normalize_units
[STOP] [2020-07-22 15:10:37] normalize_units
[START] [2020-07-22 15:10:37] calculate_statistics
[2020-07-22 15:10:37] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 15:10:37] calculate_statistics
[START] [2020-07-22 15:10:37] complete_harvest_instance
[START] [2020-07-22 15:10:37] overall_tsv_creation
[INFO] [2020-07-22 15:10:37] Processing group of 12 in 1 batches of 10000
[INFO] [2020-07-22 15:11:26] 12 Traits (unfiltered)...
[INFO] [2020-07-22 15:12:01] 12 Traits (filtered)...
[INFO] [2020-07-22 15:12:01] 0 Associations (filtered)...
[INFO] [2020-07-22 15:12:01] 27 metadata added.
[INFO] [2020-07-22 15:12:01] 0 metadata added.
[INFO] [2020-07-22 15:12:01] Average Time: 57.24
[INFO] [2020-07-22 15:12:01] Total Time: 1m24s
[STOP] [2020-07-22 15:12:01] overall_tsv_creation
[INFO] [2020-07-22 15:12:01] Done. Check your files:
[INFO] [2020-07-22 15:12:01] (12 lines) /app/public/data/snyder_snyder_19/publish_nodes.tsv
[INFO] [2020-07-22 15:12:01] (12 lines) /app/public/data/snyder_snyder_19/publish_scientific_names.tsv
[INFO] [2020-07-22 15:12:01] (13 lines) /app/public/data/snyder_snyder_19/publish_traits.tsv
[INFO] [2020-07-22 15:12:01] (4 lines) /app/public/data/snyder_snyder_19/publish_metadata.tsv
[STOP] [2020-07-22 15:12:01] complete_harvest_instance
[START] [2020-07-22 15:12:01] completed
[STOP] [2020-07-22 15:12:01] completed
[STOP] [2020-07-22 15:12:01] logged process, took 93.74
Latest Process

22 Jul 15:10 EXITED currently processing 0