Harvest for Kanda and Tsuruta 1995 Created 16 Jun 09:13

Stage: completed
Fetched: 16 Jun 09:13
Validated: 16 Jun 09:13
Deltas Created 16 Jun 09:13
Units Normalized: 16 Jun 09:14
Ancestry Built: 16 Jun 09:14
Nodes Matched: 16 Jun 09:14
Names Parsed: 16 Jun 09:14
New Models Stored: 16 Jun 09:13
Indexed: 16 Jun 09:14
Completed: 16 Jun 09:16
Time to Harvest: less than a minute
Harvesting Log

(127 lines)
# Logfile created on 2020-06-16 09:13:46 -0400 by logger.rb/v1.4.2
[INFO] [2020-06-16 09:13:46] ## HARVEST: type = -harvest
[START] [2020-06-16 09:13:51] logged process
[START] [2020-06-16 09:13:51] create_harvest_instance
[STOP] [2020-06-16 09:13:52] create_harvest_instance
[START] [2020-06-16 09:13:52] fetch_files
[STOP] [2020-06-16 09:13:52] fetch_files
[START] [2020-06-16 09:13:52] validate_each_file
[STOP] [2020-06-16 09:13:52] validate_each_file
[START] [2020-06-16 09:13:52] convert_to_csv
[CMD] [2020-06-16 09:13:52] /usr/bin/sort /app/public/converted_csv/kanda_tsuruta_ka_nodes_21280.csv > /app/public/converted_csv/kanda_tsuruta_ka_nodes_21280.csv_sorted
[CMD] [2020-06-16 09:13:52] /usr/bin/sort /app/public/converted_csv/kanda_tsuruta_ka_occurrences_21281.csv > /app/public/converted_csv/kanda_tsuruta_ka_occurrences_21281.csv_sorted
[CMD] [2020-06-16 09:13:52] /usr/bin/sort /app/public/converted_csv/kanda_tsuruta_ka_measurements_21282.csv > /app/public/converted_csv/kanda_tsuruta_ka_measurements_21282.csv_sorted
[STOP] [2020-06-16 09:13:52] convert_to_csv
[START] [2020-06-16 09:13:52] calculate_delta
[CMD] [2020-06-16 09:13:52] echo "0a" > /app/public/diff/kanda_tsuruta_ka_nodes_21280.diff
[CMD] [2020-06-16 09:13:52] tail -n +1 /app/public/converted_csv/kanda_tsuruta_ka_nodes_21280.csv >> /app/public/diff/kanda_tsuruta_ka_nodes_21280.diff
[CMD] [2020-06-16 09:13:52] echo "." >> /app/public/diff/kanda_tsuruta_ka_nodes_21280.diff
[CMD] [2020-06-16 09:13:52] echo "0a" > /app/public/diff/kanda_tsuruta_ka_occurrences_21281.diff
[CMD] [2020-06-16 09:13:52] tail -n +1 /app/public/converted_csv/kanda_tsuruta_ka_occurrences_21281.csv >> /app/public/diff/kanda_tsuruta_ka_occurrences_21281.diff
[CMD] [2020-06-16 09:13:52] echo "." >> /app/public/diff/kanda_tsuruta_ka_occurrences_21281.diff
[CMD] [2020-06-16 09:13:52] echo "0a" > /app/public/diff/kanda_tsuruta_ka_measurements_21282.diff
[CMD] [2020-06-16 09:13:52] tail -n +1 /app/public/converted_csv/kanda_tsuruta_ka_measurements_21282.csv >> /app/public/diff/kanda_tsuruta_ka_measurements_21282.diff
[CMD] [2020-06-16 09:13:52] echo "." >> /app/public/diff/kanda_tsuruta_ka_measurements_21282.diff
[STOP] [2020-06-16 09:13:52] calculate_delta
[START] [2020-06-16 09:13:52] parse_diff_and_store
[INFO] [2020-06-16 09:13:52] Loading nodes diff file into memory (true lines)...
[INFO] [2020-06-16 09:13:53] Loading occurrences diff file into memory (true lines)...
[INFO] [2020-06-16 09:13:53] Loading measurements diff file into memory (true lines)...
[INFO] [2020-06-16 09:13:53] Storing 66 ScientificNames
[INFO] [2020-06-16 09:13:53] Processing group of 66 in 1 groups of 1000
[INFO] [2020-06-16 09:13:53] Average Time: 0.04
[INFO] [2020-06-16 09:13:53] Total Time: 1s
[INFO] [2020-06-16 09:13:53] Storing 66 Nodes
[INFO] [2020-06-16 09:13:53] Processing group of 66 in 1 groups of 1000
[INFO] [2020-06-16 09:13:53] Average Time: 0.02
[INFO] [2020-06-16 09:13:53] Total Time: 1s
[INFO] [2020-06-16 09:13:53] Storing 42 Occurrences
[INFO] [2020-06-16 09:13:53] Processing group of 42 in 1 groups of 1000
[INFO] [2020-06-16 09:13:53] Average Time: 0.01
[INFO] [2020-06-16 09:13:53] Total Time: 1s
[INFO] [2020-06-16 09:13:53] Storing 84 Traits
[INFO] [2020-06-16 09:13:53] Processing group of 84 in 1 groups of 1000
[INFO] [2020-06-16 09:13:53] Average Time: 0.03
[INFO] [2020-06-16 09:13:53] Total Time: 1s
[INFO] [2020-06-16 09:13:53] Storing 168 MetaTraits
[INFO] [2020-06-16 09:13:53] Processing group of 168 in 1 groups of 1000
[INFO] [2020-06-16 09:13:53] Average Time: 0.02
[INFO] [2020-06-16 09:13:53] Total Time: 1s
[STOP] [2020-06-16 09:13:53] parse_diff_and_store
[START] [2020-06-16 09:13:53] resolve_keys
[INFO] [2020-06-16 09:14:00] Occurrences to nodes (through scientific_names)...
[INFO] [2020-06-16 09:14:00] traits to occurrences...
[INFO] [2020-06-16 09:14:00] traits to nodes (through occurrences)...
[INFO] [2020-06-16 09:14:00] Traits to sex term...
[INFO] [2020-06-16 09:14:00] Traits to lifestage term...
[INFO] [2020-06-16 09:14:00] MetaTraits to traits...
[INFO] [2020-06-16 09:14:00] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2020-06-16 09:14:00] Assocs to occurrences...
[INFO] [2020-06-16 09:14:00] Assocs to nodes...
[INFO] [2020-06-16 09:14:00] Assoc to sex term...
[INFO] [2020-06-16 09:14:00] Assoc to lifestage term...
[STOP] [2020-06-16 09:14:00] resolve_keys
[START] [2020-06-16 09:14:01] hold_for_later_1
[STOP] [2020-06-16 09:14:01] hold_for_later_1
[START] [2020-06-16 09:14:01] hold_for_later_2
[STOP] [2020-06-16 09:14:01] hold_for_later_2
[START] [2020-06-16 09:14:01] resolve_missing_parents
[STOP] [2020-06-16 09:14:01] resolve_missing_parents
[START] [2020-06-16 09:14:01] rebuild_nodes
[START] [2020-06-16 09:14:01] Flattener#flatten
[START] [2020-06-16 09:14:01] Flattener#study_resource
[START] [2020-06-16 09:14:01] Flattener#build_ancestry
[STOP] [2020-06-16 09:14:01] Flattener#build_ancestry
[INFO] [2020-06-16 09:14:01] 66 ancestry keys
[START] [2020-06-16 09:14:01] build_node_ancestors
[INFO] [2020-06-16 09:14:01] old ancestors deleted.
[STOP] [2020-06-16 09:14:01] build_node_ancestors
[START] [2020-06-16 09:14:01] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:14:01] Flattener#propagate_ancestor_ids
[STOP] [2020-06-16 09:14:01] Flattener#flatten
[STOP] [2020-06-16 09:14:01] rebuild_nodes
[START] [2020-06-16 09:14:01] resolve_missing_media_owners
[STOP] [2020-06-16 09:14:01] resolve_missing_media_owners
[START] [2020-06-16 09:14:01] sanitize_media_verbatims
[STOP] [2020-06-16 09:14:01] sanitize_media_verbatims
[START] [2020-06-16 09:14:01] queue_downloads
[STOP] [2020-06-16 09:14:01] queue_downloads
[START] [2020-06-16 09:14:01] parse_names
[WARN] [2020-06-16 09:14:01] I see 66 names which still need to be parsed.
[STOP] [2020-06-16 09:14:02] parse_names
[START] [2020-06-16 09:14:02] denormalize_canonical_names_to_nodes
[STOP] [2020-06-16 09:14:02] denormalize_canonical_names_to_nodes
[START] [2020-06-16 09:14:02] match_nodes
[START] [2020-06-16 09:14:02] map_all_nodes_to_pages
[STOP] [2020-06-16 09:14:20] map_all_nodes_to_pages
[INFO] [2020-06-16 09:14:20] 16 Unmatched nodes (of 66)! That's too many to output. First 10: Campanualaceae (#80097727); Capparidaceae (#80097728); Alsola komarovi (#80097718); Compositae (#80097734); Cruciferae (#80097736); Brassica rapo (#80097726); Raphanus sativa (#80097769); Cucumis sativa (#80097739); Cyclobalanopsis myrsinaefolia (#80097742); Gramineae (#80097752)
[START] [2020-06-16 09:14:20] update_nodes
[STOP] [2020-06-16 09:14:20] update_nodes
[STOP] [2020-06-16 09:14:20] match_nodes
[START] [2020-06-16 09:14:20] reindex_search
[STOP] [2020-06-16 09:14:20] reindex_search
[START] [2020-06-16 09:14:20] normalize_units
[STOP] [2020-06-16 09:14:20] normalize_units
[START] [2020-06-16 09:14:20] calculate_statistics
[STOP] [2020-06-16 09:14:20] calculate_statistics
[START] [2020-06-16 09:14:20] complete_harvest_instance
[START] [2020-06-16 09:14:20] overall_tsv_creation
[INFO] [2020-06-16 09:14:20] Processing group of 66 in 1 batches of 10000
[INFO] [2020-06-16 09:15:11] 42 Traits (unfiltered)...
[INFO] [2020-06-16 09:15:24] 42 Traits (filtered)...
[INFO] [2020-06-16 09:15:24] 0 Associations (filtered)...
[INFO] [2020-06-16 09:16:02] 168 metadata added.
[INFO] [2020-06-16 09:16:02] 0 metadata added.
[INFO] [2020-06-16 09:16:02] Average Time: 72.72
[INFO] [2020-06-16 09:16:02] Total Time: 1m42s
[STOP] [2020-06-16 09:16:02] overall_tsv_creation
[INFO] [2020-06-16 09:16:02] Done. Check your files:
[INFO] [2020-06-16 09:16:02] (66 lines) /app/public/data/kanda_tsuruta_ka/publish_nodes.tsv
[INFO] [2020-06-16 09:16:02] (107 lines) /app/public/data/kanda_tsuruta_ka/publish_node_ancestors.tsv
[INFO] [2020-06-16 09:16:02] (66 lines) /app/public/data/kanda_tsuruta_ka/publish_scientific_names.tsv
[INFO] [2020-06-16 09:16:02] (43 lines) /app/public/data/kanda_tsuruta_ka/publish_traits.tsv
[INFO] [2020-06-16 09:16:02] (169 lines) /app/public/data/kanda_tsuruta_ka/publish_metadata.tsv
[STOP] [2020-06-16 09:16:02] complete_harvest_instance
[START] [2020-06-16 09:16:02] completed
[STOP] [2020-06-16 09:16:02] completed
[STOP] [2020-06-16 09:16:02] logged process, took 130.46
Latest Process

16 Jun 09:13 EXITED currently processing 0