Harvest for HABIB 2010 Created 22 Jul 15:26

Stage: completed
Fetched: 22 Jul 15:26
Validated: 22 Jul 15:26
Deltas Created 22 Jul 15:26
Units Normalized: 22 Jul 15:26
Ancestry Built: 22 Jul 15:26
Nodes Matched: 22 Jul 15:26
Names Parsed: 22 Jul 15:26
New Models Stored: 22 Jul 15:26
Indexed: 22 Jul 15:26
Completed: 22 Jul 15:28
Time to Harvest: less than a minute

Harvesting Log

(132 lines)
# Logfile created on 2020-07-22 15:20:32 -0400 by logger.rb/v1.4.2
[START] [2020-07-22 15:20:32] logged process
[START] [2020-07-22 15:20:32] Creating resource from OpenData
[START] [2020-07-22 15:20:32] logged process
[START] [2020-07-22 15:20:32] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:20:32] Parse meta.xml file and create formats with fields
[STOP] [2020-07-22 15:20:32] Creating resource from OpenData
[INFO] [2020-07-22 15:26:43] ## HARVEST: type = -harvest
[START] [2020-07-22 15:26:44] logged process
[START] [2020-07-22 15:26:44] create_harvest_instance
[STOP] [2020-07-22 15:26:45] create_harvest_instance
[START] [2020-07-22 15:26:45] fetch_files
[STOP] [2020-07-22 15:26:45] fetch_files
[START] [2020-07-22 15:26:45] validate_each_file
[STOP] [2020-07-22 15:26:45] validate_each_file
[START] [2020-07-22 15:26:45] convert_to_csv
[CMD] [2020-07-22 15:26:45] /usr/bin/sort /app/public/converted_csv/habib_2010_habib_nodes_22087.csv > /app/public/converted_csv/habib_2010_habib_nodes_22087.csv_sorted
[CMD] [2020-07-22 15:26:45] /usr/bin/sort /app/public/converted_csv/habib_2010_habib_occurrences_22088.csv > /app/public/converted_csv/habib_2010_habib_occurrences_22088.csv_sorted
[CMD] [2020-07-22 15:26:45] /usr/bin/sort /app/public/converted_csv/habib_2010_habib_measurements_22089.csv > /app/public/converted_csv/habib_2010_habib_measurements_22089.csv_sorted
[STOP] [2020-07-22 15:26:45] convert_to_csv
[START] [2020-07-22 15:26:45] calculate_delta
[CMD] [2020-07-22 15:26:45] echo "0a" > /app/public/diff/habib_2010_habib_nodes_22087.diff
[CMD] [2020-07-22 15:26:45] tail -n +1 /app/public/converted_csv/habib_2010_habib_nodes_22087.csv >> /app/public/diff/habib_2010_habib_nodes_22087.diff
[CMD] [2020-07-22 15:26:45] echo "." >> /app/public/diff/habib_2010_habib_nodes_22087.diff
[CMD] [2020-07-22 15:26:45] echo "0a" > /app/public/diff/habib_2010_habib_occurrences_22088.diff
[CMD] [2020-07-22 15:26:45] tail -n +1 /app/public/converted_csv/habib_2010_habib_occurrences_22088.csv >> /app/public/diff/habib_2010_habib_occurrences_22088.diff
[CMD] [2020-07-22 15:26:45] echo "." >> /app/public/diff/habib_2010_habib_occurrences_22088.diff
[CMD] [2020-07-22 15:26:45] echo "0a" > /app/public/diff/habib_2010_habib_measurements_22089.diff
[CMD] [2020-07-22 15:26:45] tail -n +1 /app/public/converted_csv/habib_2010_habib_measurements_22089.csv >> /app/public/diff/habib_2010_habib_measurements_22089.diff
[CMD] [2020-07-22 15:26:45] echo "." >> /app/public/diff/habib_2010_habib_measurements_22089.diff
[STOP] [2020-07-22 15:26:45] calculate_delta
[START] [2020-07-22 15:26:45] parse_diff_and_store
[INFO] [2020-07-22 15:26:45] Loading nodes diff file into memory (true lines)...
[INFO] [2020-07-22 15:26:45] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-07-22 15:26:45] Loading measurements diff file into memory (true lines)...
[INFO] [2020-07-22 15:26:45] Storing 7 ScientificNames
[INFO] [2020-07-22 15:26:45] Processing group of 7 in 1 groups of 1000
[INFO] [2020-07-22 15:26:45] Average Time: 0.01
[INFO] [2020-07-22 15:26:45] Total Time: 1s
[INFO] [2020-07-22 15:26:45] Storing 7 Nodes
[INFO] [2020-07-22 15:26:45] Processing group of 7 in 1 groups of 1000
[INFO] [2020-07-22 15:26:45] Average Time: 0.0
[INFO] [2020-07-22 15:26:45] Total Time: 1s
[INFO] [2020-07-22 15:26:45] Storing 7 Occurrences
[INFO] [2020-07-22 15:26:45] Processing group of 7 in 1 groups of 1000
[INFO] [2020-07-22 15:26:45] Average Time: 0.0
[INFO] [2020-07-22 15:26:45] Total Time: 1s
[INFO] [2020-07-22 15:26:45] Storing 14 Traits
[INFO] [2020-07-22 15:26:45] Processing group of 14 in 1 groups of 1000
[INFO] [2020-07-22 15:26:45] Average Time: 0.01
[INFO] [2020-07-22 15:26:45] Total Time: 1s
[INFO] [2020-07-22 15:26:45] Storing 21 MetaTraits
[INFO] [2020-07-22 15:26:45] Processing group of 21 in 1 groups of 1000
[INFO] [2020-07-22 15:26:45] Average Time: 0.0
[INFO] [2020-07-22 15:26:45] Total Time: 1s
[STOP] [2020-07-22 15:26:45] parse_diff_and_store
[START] [2020-07-22 15:26:45] resolve_keys
[INFO] [2020-07-22 15:26:52] Occurrences to nodes (through scientific_names)...
[INFO] [2020-07-22 15:26:52] traits to occurrences...
[INFO] [2020-07-22 15:26:52] traits to nodes (through occurrences)...
[INFO] [2020-07-22 15:26:52] Traits to sex term...
[INFO] [2020-07-22 15:26:52] Traits to lifestage term...
[INFO] [2020-07-22 15:26:52] MetaTraits to traits...
[INFO] [2020-07-22 15:26:52] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-07-22 15:26:52] Assocs to occurrences...
[INFO] [2020-07-22 15:26:52] Assocs to nodes...
[INFO] [2020-07-22 15:26:52] Assoc to sex term...
[INFO] [2020-07-22 15:26:52] Assoc to lifestage term...
[STOP] [2020-07-22 15:26:52] resolve_keys
[START] [2020-07-22 15:26:52] hold_for_later_1
[STOP] [2020-07-22 15:26:52] hold_for_later_1
[START] [2020-07-22 15:26:52] hold_for_later_2
[STOP] [2020-07-22 15:26:52] hold_for_later_2
[START] [2020-07-22 15:26:52] resolve_missing_parents
[STOP] [2020-07-22 15:26:52] resolve_missing_parents
[START] [2020-07-22 15:26:52] rebuild_nodes
[START] [2020-07-22 15:26:52] Flattener#flatten
[START] [2020-07-22 15:26:52] Flattener#study_resource
[START] [2020-07-22 15:26:52] Flattener#build_ancestry
[STOP] [2020-07-22 15:26:52] Flattener#build_ancestry
[INFO] [2020-07-22 15:26:52] 7 ancestry keys
[START] [2020-07-22 15:26:52] build_node_ancestors
[INFO] [2020-07-22 15:26:52] old ancestors deleted.
[STOP] [2020-07-22 15:26:52] build_node_ancestors
[WARN] [2020-07-22 15:26:52] Flattener: nothing to flatten! (Completely flat resource?)
[STOP] [2020-07-22 15:26:52] Flattener#flatten
[STOP] [2020-07-22 15:26:52] rebuild_nodes
[START] [2020-07-22 15:26:52] resolve_missing_media_owners
[STOP] [2020-07-22 15:26:52] resolve_missing_media_owners
[START] [2020-07-22 15:26:52] sanitize_media_verbatims
[STOP] [2020-07-22 15:26:52] sanitize_media_verbatims
[START] [2020-07-22 15:26:52] queue_downloads
[STOP] [2020-07-22 15:26:52] queue_downloads
[START] [2020-07-22 15:26:52] parse_names
[WARN] [2020-07-22 15:26:52] I see 7 names which still need to be parsed.
[STOP] [2020-07-22 15:26:53] parse_names
[START] [2020-07-22 15:26:53] denormalize_canonical_names_to_nodes
[STOP] [2020-07-22 15:26:53] denormalize_canonical_names_to_nodes
[START] [2020-07-22 15:26:53] match_nodes
[START] [2020-07-22 15:26:53] map_all_nodes_to_pages
[STOP] [2020-07-22 15:26:53] map_all_nodes_to_pages
[INFO] [2020-07-22 15:26:53] ZERO unmatched nodes (of 7)! Nicely done.
[START] [2020-07-22 15:26:53] update_nodes
[STOP] [2020-07-22 15:26:53] update_nodes
[STOP] [2020-07-22 15:26:53] match_nodes
[START] [2020-07-22 15:26:53] reindex_search
[STOP] [2020-07-22 15:26:53] reindex_search
[START] [2020-07-22 15:26:53] normalize_units
[STOP] [2020-07-22 15:26:53] normalize_units
[START] [2020-07-22 15:26:53] calculate_statistics
[2020-07-22 15:26:53] ZERO NODE ANCESTORS. Is this actually a completely flat resource?
[STOP] [2020-07-22 15:26:53] calculate_statistics
[START] [2020-07-22 15:26:53] complete_harvest_instance
[START] [2020-07-22 15:26:53] overall_tsv_creation
[INFO] [2020-07-22 15:26:53] Processing group of 7 in 1 batches of 10000
[INFO] [2020-07-22 15:27:42] 7 Traits (unfiltered)...
[INFO] [2020-07-22 15:28:19] 7 Traits (filtered)...
[INFO] [2020-07-22 15:28:19] 0 Associations (filtered)...
[INFO] [2020-07-22 15:28:19] 28 metadata added.
[INFO] [2020-07-22 15:28:19] 0 metadata added.
[INFO] [2020-07-22 15:28:19] Average Time: 58.07
[INFO] [2020-07-22 15:28:19] Total Time: 1m26s
[STOP] [2020-07-22 15:28:19] overall_tsv_creation
[INFO] [2020-07-22 15:28:19] Done. Check your files:
[INFO] [2020-07-22 15:28:19] (7 lines) /app/public/data/habib_2010_habib/publish_nodes.tsv
[INFO] [2020-07-22 15:28:19] (7 lines) /app/public/data/habib_2010_habib/publish_scientific_names.tsv
[INFO] [2020-07-22 15:28:19] (8 lines) /app/public/data/habib_2010_habib/publish_traits.tsv
[INFO] [2020-07-22 15:28:19] (8 lines) /app/public/data/habib_2010_habib/publish_metadata.tsv
[STOP] [2020-07-22 15:28:19] complete_harvest_instance
[START] [2020-07-22 15:28:19] completed
[STOP] [2020-07-22 15:28:19] completed
[STOP] [2020-07-22 15:28:19] logged process, took 95.1

Latest Process