Harvest for Alexander 2004 Created 22 Jul 14:43

Stage: completed
Fetched: 22 Jul 14:43
Validated: 22 Jul 14:43
Deltas Created 22 Jul 14:43
Units Normalized: 22 Jul 14:43
Ancestry Built: 22 Jul 14:43
Nodes Matched: 22 Jul 14:43
Names Parsed: 22 Jul 14:43
New Models Stored: 22 Jul 14:43
Indexed: 22 Jul 14:43
Completed: 22 Jul 14:45
Time to Harvest: less than a minute
Harvesting Log

(132 lines)
# Logfile created on 2020-07-22 14:41:46 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 14:41:46] logged process
[START] [2020-07-22 14:41:46] Creating resource from OpenData
[START] [2020-07-22 14:41:46] logged process
[START] [2020-07-22 14:41:46] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:41:46] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 14:41:46] Creating resource from OpenData
[INFO] [2020-07-22 14:43:33] ## HARVEST: type = -harvest
[START] [2020-07-22 14:43:34] logged process
[START] [2020-07-22 14:43:34] create_harvest_instance
[STOP] [2020-07-22 14:43:35] create_harvest_instance
[START] [2020-07-22 14:43:35] fetch_files
[STOP] [2020-07-22 14:43:35] fetch_files
[START] [2020-07-22 14:43:35] validate_each_file
[STOP] [2020-07-22 14:43:36] validate_each_file
[START] [2020-07-22 14:43:36] convert_to_csv
[CMD] [2020-07-22 14:43:36] /usr/bin/sort /app/public/converted_csv/alexander_alexan_nodes_21997.csv > /app/public/converted_csv/alexander_alexan_nodes_21997.csv_sorted
[CMD] [2020-07-22 14:43:36] /usr/bin/sort /app/public/converted_csv/alexander_alexan_occurrences_21998.csv > /app/public/converted_csv/alexander_alexan_occurrences_21998.csv_sorted
[CMD] [2020-07-22 14:43:36] /usr/bin/sort /app/public/converted_csv/alexander_alexan_measurements_21999.csv > /app/public/converted_csv/alexander_alexan_measurements_21999.csv_sorted
[STOP] [2020-07-22 14:43:36] convert_to_csv
[START] [2020-07-22 14:43:36] calculate_delta
[CMD] [2020-07-22 14:43:36] echo "0a" > /app/public/diff/alexander_alexan_nodes_21997.diff
[CMD] [2020-07-22 14:43:36] tail -n +1 /app/public/converted_csv/alexander_alexan_nodes_21997.csv >> /app/public/diff/alexander_alexan_nodes_21997.diff
[CMD] [2020-07-22 14:43:36] echo "." >> /app/public/diff/alexander_alexan_nodes_21997.diff
[CMD] [2020-07-22 14:43:36] echo "0a" > /app/public/diff/alexander_alexan_occurrences_21998.diff
[CMD] [2020-07-22 14:43:36] tail -n +1 /app/public/converted_csv/alexander_alexan_occurrences_21998.csv >> /app/public/diff/alexander_alexan_occurrences_21998.diff
[CMD] [2020-07-22 14:43:36] echo "." >> /app/public/diff/alexander_alexan_occurrences_21998.diff
[CMD] [2020-07-22 14:43:36] echo "0a" > /app/public/diff/alexander_alexan_measurements_21999.diff
[CMD] [2020-07-22 14:43:36] tail -n +1 /app/public/converted_csv/alexander_alexan_measurements_21999.csv >> /app/public/diff/alexander_alexan_measurements_21999.diff
[CMD] [2020-07-22 14:43:36] echo "." >> /app/public/diff/alexander_alexan_measurements_21999.diff
[STOP] [2020-07-22 14:43:36] calculate_delta
[START] [2020-07-22 14:43:36] parse_diff_and_store
[INFO] [2020-07-22 14:43:36] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 14:43:36] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 14:43:36] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 14:43:36] Storing 2 ScientificNames
[INFO] [2020-07-22 14:43:36] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 14:43:36] Average Time: 0.0
[INFO] [2020-07-22 14:43:36] Total Time: 1s
[INFO] [2020-07-22 14:43:36] Storing 2 Nodes
[INFO] [2020-07-22 14:43:36] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 14:43:36] Average Time: 0.0
[INFO] [2020-07-22 14:43:36] Total Time: 1s
[INFO] [2020-07-22 14:43:36] Storing 2 Occurrences
[INFO] [2020-07-22 14:43:36] Processing group of 2 in 1 groups of 1000
[INFO] [2020-07-22 14:43:36] Average Time: 0.0
[INFO] [2020-07-22 14:43:36] Total Time: 1s
[INFO] [2020-07-22 14:43:36] Storing 5 Traits
[INFO] [2020-07-22 14:43:36] Processing group of 5 in 1 groups of 1000
[INFO] [2020-07-22 14:43:36] Average Time: 0.0
[INFO] [2020-07-22 14:43:36] Total Time: 1s
[INFO] [2020-07-22 14:43:36] Storing 5 MetaTraits
[INFO] [2020-07-22 14:43:36] Processing group of 5 in 1 groups of 1000
[INFO] [2020-07-22 14:43:36] Average Time: 0.0
[INFO] [2020-07-22 14:43:36] Total Time: 1s
[STOP] [2020-07-22 14:43:36] parse_diff_and_store
[START] [2020-07-22 14:43:36] resolve_keys
[INFO] [2020-07-22 14:43:43] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 14:43:43] traits to occurrences...
[INFO] [2020-07-22 14:43:43] traits to nodes (through occurrences)...
[INFO] [2020-07-22 14:43:43] Traits to sex term...
[INFO] [2020-07-22 14:43:43] Traits to lifestage term...
[INFO] [2020-07-22 14:43:43] MetaTraits to traits...
[INFO] [2020-07-22 14:43:43] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 14:43:43] Assocs to occurrences...
[INFO] [2020-07-22 14:43:43] Assocs to nodes...
[INFO] [2020-07-22 14:43:43] Assoc to sex term...
[INFO] [2020-07-22 14:43:43] Assoc to lifestage term...
[STOP] [2020-07-22 14:43:43] resolve_keys
[START] [2020-07-22 14:43:43] hold_for_later_1
[STOP] [2020-07-22 14:43:43] hold_for_later_1
[START] [2020-07-22 14:43:43] hold_for_later_2
[STOP] [2020-07-22 14:43:43] hold_for_later_2
[START] [2020-07-22 14:43:43] resolve_missing_parents
[STOP] [2020-07-22 14:43:43] resolve_missing_parents
[START] [2020-07-22 14:43:43] rebuild_nodes
[START] [2020-07-22 14:43:43] Flattener#flatten
[START] [2020-07-22 14:43:43] Flattener#study_resource
[START] [2020-07-22 14:43:43] Flattener#build_ancestry
[STOP] [2020-07-22 14:43:43] Flattener#build_ancestry
[INFO] [2020-07-22 14:43:43] 2 ancestry keys
[START] [2020-07-22 14:43:43] build_node_ancestors
[INFO] [2020-07-22 14:43:43] old ancestors deleted.
[STOP] [2020-07-22 14:43:43] build_node_ancestors
[WARN] [2020-07-22 14:43:43] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 14:43:43] Flattener#flatten
[STOP] [2020-07-22 14:43:43] rebuild_nodes
[START] [2020-07-22 14:43:43] resolve_missing_media_owners
[STOP] [2020-07-22 14:43:43] resolve_missing_media_owners
[START] [2020-07-22 14:43:43] sanitize_media_verbatims
[STOP] [2020-07-22 14:43:43] sanitize_media_verbatims
[START] [2020-07-22 14:43:43] queue_downloads
[STOP] [2020-07-22 14:43:43] queue_downloads
[START] [2020-07-22 14:43:43] parse_names
[WARN] [2020-07-22 14:43:43] I see 2 names which still need to be parsed.
[STOP] [2020-07-22 14:43:44] parse_names
[START] [2020-07-22 14:43:44] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 14:43:44] denormalize_canonical_names_to_nodes
[START] [2020-07-22 14:43:44] match_nodes
[START] [2020-07-22 14:43:44] map_all_nodes_to_pages
[STOP] [2020-07-22 14:43:44] map_all_nodes_to_pages
[INFO] [2020-07-22 14:43:44] ZERO unmatched nodes (of 2)! Nicely done.
[START] [2020-07-22 14:43:44] update_nodes
[STOP] [2020-07-22 14:43:44] update_nodes
[STOP] [2020-07-22 14:43:44] match_nodes
[START] [2020-07-22 14:43:44] reindex_search
[STOP] [2020-07-22 14:43:44] reindex_search
[START] [2020-07-22 14:43:44] normalize_units
[STOP] [2020-07-22 14:43:44] normalize_units
[START] [2020-07-22 14:43:44] calculate_statistics
[2020-07-22 14:43:44] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 14:43:44] calculate_statistics
[START] [2020-07-22 14:43:44] complete_harvest_instance
[START] [2020-07-22 14:43:44] overall_tsv_creation
[INFO] [2020-07-22 14:43:44] Processing group of 2 in 1 batches of 10000
[INFO] [2020-07-22 14:44:33] 2 Traits (unfiltered)...
[INFO] [2020-07-22 14:45:09] 2 Traits (filtered)...
[INFO] [2020-07-22 14:45:09] 0 Associations (filtered)...
[INFO] [2020-07-22 14:45:09] 8 metadata added.
[INFO] [2020-07-22 14:45:09] 0 metadata added.
[INFO] [2020-07-22 14:45:09] Average Time: 57.91
[INFO] [2020-07-22 14:45:09] Total Time: 1m26s
[STOP] [2020-07-22 14:45:09] overall_tsv_creation
[INFO] [2020-07-22 14:45:09] Done. Check your files:
[INFO] [2020-07-22 14:45:09] (2 lines) /app/public/data/alexander_alexan/publish_nodes.tsv
[INFO] [2020-07-22 14:45:09] (2 lines) /app/public/data/alexander_alexan/publish_scientific_names.tsv
[INFO] [2020-07-22 14:45:09] (3 lines) /app/public/data/alexander_alexan/publish_traits.tsv
[INFO] [2020-07-22 14:45:09] (4 lines) /app/public/data/alexander_alexan/publish_metadata.tsv
[STOP] [2020-07-22 14:45:09] complete_harvest_instance
[START] [2020-07-22 14:45:09] completed
[STOP] [2020-07-22 14:45:09] completed
[STOP] [2020-07-22 14:45:09] logged process, took 94.75
Latest Process

22 Jul 14:43 EXITED currently processing 0